Thank you all!
I managed to re-tap and helicoil the hole with the manifold in place and everything is fine now. Mounted the EGR as it is supposed to. Also cleaned the MAP which was really clogged with oily soot.
So far these last 2 days no errors from the ECU, although as I saw from monitoring connected while driving, there is still overboost. In every rpm. Sometimes going even up to 2.7 bars (while the desired at the moment is ~2.2), but I guess it's just not up there enough for the limp mode to be activated. Anyway, I guess this is for some other thread, and If anyone can point me where to look for help and how to troubleshoot I would really appreciate it. Thanks guys