okay - first thing.
throw makerbot desktop away and start using Flashprint from flashforge.
Sooooo much better. Select flashforge pro.
https://www.flashforge.com/download-center

The print area duct is important - but you are right it shouldn't effect extrusion.

Do you have the same problems with both extruders ? or just the one ?

The smart extruder is not for a replicator 2 - and if you think you've had problems, go dig up the issues they had when the 'smart' extruder machines came out.
It was almost as bad as the ender 3 !

Bed levelling is important, but again won't effect actual extrusion.
Getting the filament to stick - I really recommend Dimafix. Just wipes on and holds stuff when hot and releases when cool.
A little goes a long way and lasts a long time.

Try using flashprint and if you are still having the same issues, maybe think about changing the motherboard.
The mighty boards are great - but extrusion issues do crop up with them quite regularly (had similiar issues with my replicator clone after about 5 years of heavy use).