I currently own a 1995 2 dr 4wd geo tracker auto tranny, the rearend is messed up in it (was wrecked previously before i got it, axle bent, not sure if the housing is messed up also) I recently acquired a (unknown year) 2 dr 2wd geo tracker, manuel tranny. im wondering if i can just change out the whole rearend assy, or just get the "guts" out of the 2wd housing and put them in my 4wd housing, are the ratio's the same, does it matter? Im new to this just trying to learn all i can...Thanks for any help/ advise you can spare, It would be GREATLY appreciated!-Nicole 
I think fordem is right in that you are being advised by someone who may know less than you.
Take some photo's of what you have you think is bad (much better than a description).
If you have a bent axle from an accident, probability is that the housing is also tweaked (they are light weight as axle housings go) and I would replace the housing.
There may nothing wrong with your third member (differential piece with the ring gear in it).
As brush buster said, if you have larger tires (or plan on them) now would be the time to make the switch.
Welcome to ZW, photo's help for clarification.