first check is get the actual fault codes and do a web search /ross tech wiki.
You may have more than one issue.
I'd always be tempted to suggest flashing back to stock , and even removing modifications to get to a known working state before tuning....
engine shaking etc sounds like coilpacks, can swap between cylinders and see if misfire is in same cylinder or not.
starting sounds like fuel pressure , be it from the low pressure side (in tank pump / filter etc) or high pressure side (rail,injectors,sensors) (you can log this via vagcom , and see how it drops once the engines turned off)
multiple dash lights can often be a sign of low voltage in the entire system, so id want to check your battery voltage under load ...
you couldnt be in better hands than JKM
You seem to know your stuff, as alot of your suggested ideas on the issues correspond with what was flagged up on VAG COM.
The first time I had it VAG COM'd when it was really bad I got 12 fault codes
Have got em saved so will post em up tomorrow or so. However had the car scanned about a week ago and nothing of much interest was flagged up, but still need to get DanGB to email them over.
Wayne did dan email you the fault codes at all? Dont think the cam follower is a issue, plus AMD surely would have said something if mine was worn, plus the mileage on mine is a bit low for a worn cam follower, as I was experiencing these issues at about 5-6k in.
Edit
Fault codes
Chassis Type: 1K0
Scan: 01 03 04 08 09 15 16 17 19 25 42 44 46 52 56 62 72
VIN: Mileage: 9480km/5890miles
01-Engine -- Status: Malfunction 0010
03-ABS Brakes -- Status: Malfunction 0010
04-Steering Angle -- Status: OK 0000
08-Auto HVAC -- Status: OK 0000
09-Cent. Elect. -- Status: OK 0000
15-Airbags -- Status: OK 0000
16-Steering wheel -- Status: OK 0000
17-Instruments -- Status: OK 0000
19-CAN Gateway -- Status: OK 0000
25-Immobilizer -- Status: OK 0000
42-Door Elect, Driver -- Status: OK 0000
44-Steering Assist -- Status: OK 0000
46-Central Conv. -- Status: Malfunction 0010
52-Door Elect, Pass. -- Status: OK 0000
56-Radio -- Status: OK 0000
62-Door,Rear Left -- Status: OK 0000
72-Door, Rear Right -- Status: OK 0000
-------------------------------------------------------------------------------
Address 01: Engine Labels: 06F-907-115-AXX.lbl
Part No SW: 1P0 907 115 C HW: 8P0 907 115 B
Component: 2.0l R4/4V TFSI 0020
Revision: 5BH16--- Serial number: SEZ7Z0H4000054
Coding: 0303000318070160
Shop #: WSC 12596 024 419623
12 Faults Found:
000545 - Angle Sensor for Throttle (G188): Implausible Signal
P0221 - 008 - Implausible Signal - Intermittent
Freeze Frame:
Fault Status: 00101000
Fault Priority: 0
Fault Frequency: 2
Mileage: 9034 km
Time Indication: 0
Date: 2000.00.00
Time: 21:15:58
Freeze Frame:
RPM: 5384 /min
Load: 21.2 %
Speed: 77.0 km/h
Temperature: 84.0°C
Temperature: 34.0°C
Absolute Pres.: 1010.0 mbar
Voltage: 14.224 V
005476 - Throttle Actuator (J338): Under-Voltage during Basic Setting
P1564 - 002 - Lower Limit Exceeded - Intermittent
Freeze Frame:
Fault Status: 00100010
Fault Priority: 0
Fault Frequency: 1
Mileage: 9072 km
Time Indication: 0
Date: 2000.00.00
Time: 22:31:43
Freeze Frame:
RPM: 0 /min
Load: 100.0 %
Speed: 0.0 km/h
Temperature: 97.0°C
Temperature: 55.0°C
Absolute Pres.: 1010.0 mbar
Voltage: 10.668 V
000289 - Throttle Position Sensor (G69): Implausible Signal
P0121 - 008 - Implausible Signal - Intermittent
Freeze Frame:
Fault Status: 00101000
Fault Priority: 0
Fault Frequency: 1
Mileage: 9157 km
Time Indication: 0
Date: 2000.00.00
Time: 01:40:06
Freeze Frame:
RPM: 5046 /min
Load: 20.0 %
Speed: 65.0 km/h
Temperature: 90.0°C
Temperature: 27.0°C
Absolute Pres.: 1010.0 mbar
Voltage: 14.224 V
001287 - Idle Control System RPM: Higher than Expected.
P0507 - 001 - Upper Limit Exceeded - Intermittent
Freeze Frame:
Fault Status: 00100001
Fault Priority: 0
Fault Frequency: 2
Mileage: 9159 km
Time Indication: 0
Date: 2000.00.00
Time: 01:42:10
Freeze Frame:
RPM: 1428 /min
Load: 17.2 %
Speed: 0.0 km/h
Temperature: 85.0°C
Temperature: 28.0°C
Absolute Pres.: 1020.0 mbar
Voltage: 14.351 V
000768 - Random/Multiple Cylinder Misfire Detected
P0300 - 001 - Upper Limit Exceeded - Intermittent
Freeze Frame:
Fault Status: 00100001
Fault Priority: 0
Fault Frequency: 2
Mileage: 9304 km
Time Indication: 0
Date: 2000.00.00
Time: 00:01:42
Freeze Frame:
RPM: 6560 /min
Load: 29.0 %
Speed: 122.0 km/h
Temperature: 86.0°C
Temperature: 39.0°C
Absolute Pres.: 1020.0 mbar
Voltage: 13.970 V
000771 - Cylinder 3: Misfire Detected
P0303 - 001 - Upper Limit Exceeded - Intermittent
Freeze Frame:
Fault Status: 00100001
Fault Priority: 0
Fault Frequency: 2
Mileage: 9304 km
Time Indication: 0
Date: 2000.00.00
Time: 00:01:42
Freeze Frame:
RPM: 6560 /min
Load: 29.0 %
Speed: 122.0 km/h
Temperature: 86.0°C
Temperature: 39.0°C
Absolute Pres.: 1020.0 mbar
Voltage: 13.970 V
000770 - Cylinder 2: Misfire Detected
P0302 - 001 - Upper Limit Exceeded - Intermittent
Freeze Frame:
Fault Status: 00100001
Fault Priority: 0
Fault Frequency: 1
Mileage: 9304 km
Time Indication: 0
Date: 2000.00.00
Time: 00:01:42
Freeze Frame:
RPM: 6560 /min
Load: 29.0 %
Speed: 122.0 km/h
Temperature: 86.0°C
Temperature: 39.0°C
Absolute Pres.: 1020.0 mbar
Voltage: 13.970 V
004688 - Fuel Level too Low
P1250 - 008 - Implausible Signal
Freeze Frame:
Fault Status: 01101000
Fault Priority: 0
Fault Frequency: 1
Mileage: 9436 km
Time Indication: 0
Date: 2000.00.00
Time: 20:45:02
Freeze Frame:
RPM: 1435 /min
Load: 17.2 %
Speed: 0.0 km/h
Temperature: 85.0°C
Temperature: 28.0°C
Absolute Pres.: 1020.0 mbar
Voltage: 14.351 V
000313 - Oxygen (Lambda) Sensor B1 S2: Response too Slow
P0139 - 004 - No Signal/Communication - Intermittent
Freeze Frame:
Fault Status: 00100100
Fault Priority: 0
Fault Frequency: 1
Mileage: 9467 km
Time Indication: 0
Date: 2000.00.00
Time: 18:37:03
Freeze Frame:
RPM: 2999 /min
Load: 9.0 %
Speed: 55.0 km/h
Temperature: 83.0°C
Temperature: 41.0°C
Absolute Pres.: 1010.0 mbar
Voltage: 14.097 V
004372 - Oxygen (Lambda) Sensor; B1 S2: Internal Resistance too High
P1114 - 008 - Implausible Signal - Intermittent
Freeze Frame:
Fault Status: 00101000
Fault Priority: 0
Fault Frequency: 1
Mileage: 9467 km
Time Indication: 0
Date: 2000.00.00
Time: 18:37:03
Freeze Frame:
RPM: 2964 /min
Load: 8.6 %
Speed: 55.0 km/h
Temperature: 83.0°C
Temperature: 42.0°C
Absolute Pres.: 1010.0 mbar
Voltage: 14.097 V
005445 - Throttle Valve Controller: Malfunction
P1545 - 001 - Upper Limit Exceeded - Intermittent
Freeze Frame:
Fault Status: 00100001
Fault Priority: 0
Fault Frequency: 2
Mileage: 9467 km
Time Indication: 0
Date: 2000.00.00
Time: 18:37:08
Freeze Frame:
RPM: 1386 /min
Load: 29.8 %
Speed: 38.0 km/h
Temperature: 83.0°C
Temperature: 45.0°C
Absolute Pres.: 1010.0 mbar
Voltage: 14.097 V
005445 - Throttle Valve Controller: Malfunction
P1545 - 008 - Implausible Signal - Intermittent
Freeze Frame:
Fault Status: 00101000
Fault Priority: 0
Fault Frequency: 1
Mileage: 9467 km
Time Indication: 0
Date: 2000.00.00
Time: 18:37:09
Freeze Frame:
RPM: 1145 /min
Load: 43.1 %
Speed: 36.0 km/h
Temperature: 83.0°C
Temperature: 45.0°C
Absolute Pres.: 1010.0 mbar
Voltage: 14.097 V
Readiness: 0000 0000
-------------------------------------------------------------------------------
Address 03: ABS Brakes (-----) Labels: 1K0-907-379-60EC1F.clb
Part No SW: 1K0 907 379 AD HW: 1K0 907 379 AD
Component: ESP MK60EC1 H35 0104
Revision: 00H35001
Coding: 163B8012092500FA681201EC901D00813400
Shop #: WSC 04941 000 00000
2 Faults Found:
02214 - Tire Pressure Warning
002 - Lower Limit Exceeded - Intermittent
Freeze Frame:
Fault Status: 00100010
Fault Priority: 2
Fault Frequency: 1
Reset counter: 63
Mileage: 8389 km
Time Indication: 0
Freeze Frame:
Count: 0
Count: 32768
Count: 4608
Count: 397
Count: 50477
Count: 3
Count: 0
Count: 0
01314 - Engine Control Module
013 - Check DTC Memory - Intermittent
Freeze Frame:
Fault Status: 00101101
Fault Priority: 2
Fault Frequency: 3
Reset counter: 82
Mileage: 9034 km
Time Indication: 0
Freeze Frame:
Count: 16448
Count: 32768
Count: 12800
Count: 8196
Count: 50475
Count: 1300
Count: 256
Count: 0
-------------------------------------------------------------------------------
Address 08: Auto HVAC Labels: 1K0-907-044.lbl
Part No: 1P0 907 044 D
Component: ClimatronicPQ35 011 0702
Shop #: WSC 00000 000 00000
No fault code found.
-------------------------------------------------------------------------------
Address 09: Cent. Elect. Labels: 3C0-937-049-30-H.lbl
Part No SW: 3C8 937 049 E HW: 3C8 937 049 E
Component: Bordnetz-SG H54 2602
Revision: 00H54000 Serial number: 00000005913491
Coding: 818C0F2F00041000431D00000000000000007F075C400000000000000000
Shop #: WSC 06402 785 00200
Part No: 1P0 955 119 B
Component: Wischer 290708 022 0601
Coding: 00056208
Shop #: WSC 06402
No fault code found.
-------------------------------------------------------------------------------
Address 15: Airbags Labels: 5N0-959-655.lbl
Part No SW: 5N0 959 655 A HW: 5N0 959 655 A
Component: J234__A03 VW10 HI 1815
Revision: 19013000 Serial number: 0039DPJDFFB.
Coding: 0012339
Shop #: WSC 06402 785 00200
No fault code found.
-------------------------------------------------------------------------------
Address 16: Steering wheel Labels: 1K0-953-549-MY8.lbl
Part No SW: 1K0 953 549 BS HW: 1K0 953 549 BS
Component: J0527 752 0101
Coding: 0002042
Shop #: WSC 06402 785 00200
Part No: XXXXXXXXXXX
Component: E0221 001 0010
No fault code found.
-------------------------------------------------------------------------------
Address 17: Instruments Labels: 1K0-920-xxx-17.lbl
Part No: 1P0 920 925 C
Component: KOMBIINSTRUMENT VO3 0424
Coding: 0000401
Shop #: WSC 01108 476 96591
No fault code found.
-------------------------------------------------------------------------------
Address 19: CAN Gateway Labels: 1K0-907-530.lbl
Part No SW: 1K0 907 530 Q HW: 1K0 907 951
Component: J533__Gateway H16 0202
Revision: H16 Serial number: 2700K0890900DE
Coding: E9807F060002020203
Shop #: WSC 06402 785 00200
No fault code found.
-------------------------------------------------------------------------------
Address 25: Immobilizer Labels: 1K0-920-xxx-25.lbl
Part No: 1P0 920 925 C
Component: IMMO VO3 0424
Shop #: WSC 00000 000 00000
No fault code found.
-------------------------------------------------------------------------------
Address 42: Door Elect, Driver Labels: 1K0-959-701-MAX3.lbl
Part No SW: 1T0 959 701 L HW: 1K0 959 793 P
Component: J386 TUER-SG FT 1518
Revision: 71009005 Serial number: 00000528888531
Coding: 0004784
Shop #: WSC 06402 785 00200
No fault code found.
-------------------------------------------------------------------------------
Address 44: Steering Assist Labels: 1Kx-909-14x.lbl
Part No: 1K0 909 144 C
Component: EPS_ZFLS Kl. 154 2301
Revision: 00H15000
Shop #: WSC 06402 785 00200
No fault code found.
-------------------------------------------------------------------------------
Address 46: Central Conv. Labels: 1K0-959-433-MAX.clb
Part No SW: 1K0 959 433 BT HW: 1K0 959 433 BT
Component: KSG PQ35 G2 020 0204
Revision: 00020000 Serial number: 00000000000000
Coding: 988000005283CC7F00068F0F60085F86107C80
Shop #: WSC 06402 785 00200
Part No: 1P0 951 171
Component: Innenraumueberw.010 4971
Coding: 00000000
Shop #: WSC 06402
Part No: 1K0 951 605 C
Component: LIN BACKUP HORN H03 1301
Component: NGS n.mounted
1 Fault Found:
01135 - Interior Monitoring Sensors
004 - No Signal/Communication - Intermittent
Freeze Frame:
Fault Status: 00100100
Fault Priority: 4
Fault Frequency: 69
Reset counter: 82
Mileage: 743 km
Time Indication: 0
Date: 2000.00.00
Time: 23:23:43
-------------------------------------------------------------------------------
Address 52: Door Elect, Pass. Labels: 1K0-959-702-MAX3.lbl
Part No SW: 1T0 959 702 L HW: 1K0 959 792 P
Component: J387 TUER-SG BT 1518
Revision: 71009005 Serial number: 00000756388514
Coding: 0004784
Shop #: WSC 06402 785 00200
No fault code found.
-------------------------------------------------------------------------------
Address 56: Radio Labels: 1K0-035-1xx-56.lbl
Part No: 1P2 035 186 A
Component: Radio BVX 0007
Coding: 0040424
Shop #: WSC 06402 785 00200
No fault code found.
-------------------------------------------------------------------------------
Address 62: Door,Rear Left Labels: None
Part No SW: 1K0 959 703 AF HW: 1K0 959 795 S
Component: J388 TUER-SG HL 1401
Revision: 11006001 Serial number: 00000003366140
Coding: 0000144
Shop #: WSC 06402 785 00200
No fault code found.
-------------------------------------------------------------------------------
Address 72: Door, Rear Right Labels: None
Part No SW: 1K0 959 704 AF HW: 1K0 959 794 S
Component: J389 TUER-SG HR 1401
Revision: 11006001 Serial number: 00000003364257
Coding: 0000144
Shop #: WSC 06402 785 00200
No fault code found.
End ---------------------------------------------------------------------