ehemmmmm....
Removed the starter (that was a pita job from underneath) and got it on the bench. Seemed to work just fine.
Started to measure lots of stuff. Changed some connectors. Then realized that there was something strange going on with the voltage measurements (made some reference measurements) and finally I found that the ground screw on the gearbox was loose. "Someone" had removed it when he was looking for a good place to put the CC pump and not screwed it back completely. I had a serious chat with this "someone", fastened the screw and then it fired straight up 
Idle was perfect from the start, everything seem fine.
Now I'll just finish the looms, fasten stuff where it needs to be fastened and hopefully I'm good to go.
A small question about obdtuner, I assume that all parameters are logged even though I'm only looking at some of them, right? There might be an issue with my MAP sensor that I want Peter to take a look at.