Just as an update as it has been suggested, the board might have been warped; actually that’s not the case. The board is not warped a single bit but perfectly straight and refitting it into the macbook was no problem at all.
Although baking the board in an oven heats up the whole unit it provides equal heat distribution and using a heat gun has it’s own risks in frying the gpu and/or partial warping by unequal heat distribution if temperature and airflow are not carefully controlled .
If the board had warped, the two mounting points for each individual heatsink would have moved apart or away from each other which then would have resulted in some difficulty to screw the heatsinks back in, and not to mention the same thing would have happened to the mount of CPU/GPU heatsink as well.
But this is not the case either, all heatsinks are fitting perfectly into their mounts.
So far after a few days, the Macbook with its baked logic board runs perfectly smooth, all components are working, no hiccups at all. CPU and GPU temparatures are slightly lower which was expected due to cleaning of dust from fans and heatsink and applying fresh thermal paste.
So I would like to ask again if anybody had ever taken apart one of those logic boards an noticed that the aforementioned heatsinks for the controllers are not touching the chips.
Cheers
Alex