OK, first, the car isn't mine, it belongs to a friend who lives about 5 hours away, so, I only have limited info on it. Here is what I do know. It is a 1999 forester with a 5 speed that is bad. What I am looking for is info on which transmissions will work as a replacement, since the local yards say 1998 and 1999 only, and, of course, they don't have any. What I would like to know is, can I use earlier or later 5 speeds, even if I have to change some of the external electronics? I will be going down to his place in about 2 weeks to do the swap, if I can find a transmission that will work. Thank you in advance for any advice.

They changed to an 8 bolt bellhousing in 99. You can use a 98 or earlier trans, you just have to make note of the clutch release fork pivot location. The pivot is in a different spot on the cable release fork.

You'll only use 4 bolts in the bellhousing, Subaru did it that way for years.

 

You can use up to a 2002 trans. In 2003 they changed the front axle design and did away with the stub shafts that stick out of the trans. Technically you could use 03+ axles but that adds to the cost.

 

Try to stick to Forester 99-02 if you can to make the swap as easy as possible.

If you can't, Legacy Outback and GT models 96-98 have the correct front diff ratio and you can use them. 99-02 Outback you can use as well.

You usually have to swap things like speed sensor and reverse and neutral switches because a lot of junkyards just cut the wires on those.

I know about the 4 vs 8 bolt bell housing, because I do a lot of 2.2 swaps, I just have only ever done 2 Subaru transmission swaps, both automatic, on older legacy wagons. I just wasn't sure if there were any differences in the 99 and up 5 speeds, because the local yards all say 99 only for his forester. As for the wiring, I'll be pulling the transmission myself, so I won't have to worry about cut wires. Thank you for the info, it will be a huge help when I get ready to do this. One last question though, how do I know what ratio the front diff is, or are they all the same for the 99 to 02 forester?

Ratio is going to be model specific. Forester and Legacy Outback manual trans from those years have 4.10 ratio. Same with Legacy GT. 

A Legacy L, base, or Brighton model would have a 3.90. Most Impreza models had 3.90. 

 

There's no easy way to tell just by looking at the trans. The only way to know for sure is to count the teeth on the ring gear. There are charts online that you can check the trans number on the bellhousing against, but those arent always accurate.