Ed,
First of all, welcome to the boards!!
You bring up some good questions, hopefully somebody with a little more knowledge concering the differences in the trannys (if any) will be able to better answer them.
What I do know:
As far as gear ratios go, the "best" setup is to have a tranny with a taller GVR4 1st gear, double synchros and GM Synchromesh fluid (I've tried 4 others and believe me, Synchromesh is the ONLY fluid I put in my tranny now). The stock DSM 2-5 ratios are pretty damn good IMHO.
The 1.6 revs higher than the 2.0, but produces less torque so I would conject that if the trannys ARE different the 2.0 would be a bit stronger (DSM trannys are one of the weak links anyway).
As far as parts sourcing,
www.dsmtrader.com is an EXCELLENT place to find the extra parts you'll need to do the swap. A local parts car would be your best bet though.
With regard to the axles, I'm not sure that auto axles would work on a 5 speed (experts, please correct me if I'm wrong). I do know that FWD and AWD front components are nearly identical, if not exact, so I would expect that the front axles from a AWD would fit a FWD. The best route to go in that regard however, is to get equal length half-shafts which will all but eliminate torque steer.
Hope I didn't confuse more, and if I got something wrong, EXPERTS: please correct me.
-Kev