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 extrusion issues with my replicator clone after about 5 years of heavy use).