When you say "1.6" what vehicle are you referring to - the SQ416 or second gen 1.6 (same body style as your 2.0 - SQ420) or the SE416, which is the previous generation of Geo Trackers?
As far as I'm aware the SQ416 & SQ420 share a transmission, but it is not the same transmission that was used on the SE416s - having said that the two engines share a bell housing bolt pattern and the transmissions can be adapted to work.
One point to consider, SQ416s were I believe quite rare, SE416s were plentiful, but, they are all likely to have substantial mileage on them - have you considered rebuilding your transmission - does the problem require more than just a bearing and synchro replacement? Just my way of thought when it comes to used car parts - , better the devil you know ...