Okay, I changed the two u-joints in the rear driveshaft and reinstalled it only to be rewarded with some unpleasant low speed vibration. Noticed the front propeller shaft also has a u-joint to replace in it. Now that I have the service manuals I see no information on how to actually replace the u-joints or driveshaft orientation! I guess Subaru just wanted the mechanics to replace the driveshaft if there was a problem.
At any rate, if anyone can take a picture of their GL's driveshaft so I can make sure it gets put in right I'd appreciate it. There's a little subaru sticker on it so that would be a good part to take a picture of.
The drive shafts are not serviceable, the joints are staked in and the only way to replace them is to grind the staked portions out, since there are no snap rings or circlips that hold the joints in. (If you didn't have to do any grinding, it's possible the previous owner had a remanufactured drive shaft put in or something to that effect, since a replacement shaft from Subaru is about $400) Take the shaft out and make sure the joints all move freely, if they don't, you might have gotten a cup in too tight (You can usually knock the center part of the joint outwards to seat the cups against the clips) I don't remember if those shafts come apart in the center or not, if they do, and you took it apart in the center, take it apart, rotate the rear section of the shaft one quarter turn with respect to the front section and reassemble it and see if your vibration goes away, you probably just got the sections out of phase. Also make sure all of the bolts in the shaft are identical, and that you don't have a missing washer or something, since that will cause a vibration.
As for upgrading to power windows and locks, all the wiring for the power windows and locks is there, up under the dash. You will need to get the harnesses for the doors, door panels, regulators, power lock actuators, etc... but all the body wiring is there.