I just had the car scanned with VAGCOM. It came up with the following errors:
1. 16618 P0234 Turbocharger Overboost Condition Control limit exceeded
2. Manifold intake condition (not really sure what the exact code was)
3. Voltage Reference 'A' code (again not sure what the exact code was)
All came up as sporadic. The VW independent guy had never seen the last two codes, so he has cleared them and wants me to drive it and see if I experience turbo limp again. If I do then he will check the hose pipes.
I just had the codes 2 & 3 on with the EML on my Golf it appears this is a common fault with the intake manifold motor which controls flaps in the intake manifold for lower emissions. I suspect the full codes you had were
012599 - Intake Manifold Runner Control: Basic Setting not Completed
P3137 - 001 - Upper Limit Exceeded - Intermittent
001602 - Sensor Reference Voltage A: Circuit: Low
P0642 - 002 - Lower Limit Exceeded - Intermittent
You need to get the garage to do the following with VAGCOM/VCDS
Intake Manifold Runner
Prerequisites:
Ignition ON
Engine OFF
System voltage at least 11.0 V.
[Select]
[01 - Engine]
[Basic Settings - 04]
Group 142
[Go!]
Activate the Basic Setting.
[ON/OFF/Next]
Wait until Field 4 shows "ADP. O.K.".
[Done, Go Back]
[Close Controller, Go Back - 06]
Switch Ignition OFF for at least 60 seconds.
This should resolve the issue that caused your bottom 2 fault codes, if it doesn't work it will need to new motor/sensor (it is one part). I just carried out the adapation on mine along with the throttle body and it has improved the low down responses which I had noticed recently seemed slightly sluggish.