I have a 1998 Subaru Legacy Outback wagon that has an auto in it now, I have a friend with a wreck 1996 wagon with a 5 spd... the car he has runs and drives great (and has a wrx turbo engine in it)

 

anyways how much trouble will it be to go 5 spd in my current car?

The trouble is more to do with getting all the associated parts at once than the actual work. Youwillwant to veryify the rear diff ratio as a 5spd is going tobe a 3.9. You will need a 3.9 rear diff, the driveshaft, trans mount, and pedal/clutch assembly. It has been done lots of times and and the search function should find you some answers.

You can read over my awd & 5spd swap to get an idea of what's all involved. You won't need to worry about the AWD swap parts, just the 5spd parts.

 

http://www.surrealmirage.com/subaru/swap