I agree that you probably should not need to replace the transmission, assuming it's only an engagement issue.

Replacing pivot & fork and making sure the clutch & flywheel are proper should fix your problem providing it is not the transmission.

So, I think that's why the suggestion to replace the transmission was made.
Now maybe you should have 50/50 odds if you don't replace the transmission. It's not cheap to have a shop do the re&re so I can understand their suggestion of getting everything done - but with that level of work I think it should be guaranteed 100% fixed.

2.0NA FWD master cyl is MB911650
2.0 AWD Turbo is MB910562
This information is from the Mitsu parts searching software "CAPS".