The upgrade should be pretty much hassle-free if you're just rational about it. Any trouble or not, post vemslog, get feedback and/or improved vemscfg to upload, improve and repeat. It's a matter of a spending minutes, not hours to do it.
Either way, what I can see still requires VE table tuning before being ready to go anywhere.
At least upgrade the wiring to the starter from the battery, most likely the ECU resets and VemsTune reconnects while the engine starts. When you're cold starting it the battery is probably fresh enough so that it wont reset. It's the initial surge of current that causes the reset, dips below 8 Volts and you're in trouble.
The ECU and engine management harness can have it's own main feed from the battery, that can also fix the issues since the voltage won't drop as much at the battery. If you are already setup that way, then there is no easy fix but better wiring or a fresh new (stronger) battery.