What right side bushing are you talking about?
Alignment, unless you have a rack or you are experience with the tape measure (and extremely level floor), then I would take it somewhere.
How do you know the
tranny fluid is dark? Isn't this a 5 speed car? Anyways, changing
tranny fluid on manual
trans stangs is easy. I do it by removing both plugs on the side of the
tranny (3/8 square drive heads). And by removing the shifter. This method takes a little longer, but to me its much cleaner, and much easier then running a funnel with a hose from the engine bay. Once the fluid is drained, re-install bottom plug, leave out top plug. Fill the
tranny through the shifter hole, it will take about 2.5 quarts of ATF (mercon 5), once it starts draining out of the top plug hole its full. Re-silicone the shifter base and put the shifter back in.
The squeeking is probably the throw-out bearing. My advice is that if you want to change it, you might as well do the whole clutch, you have to pull the
trans either way. For $400 you can get a very good performance clutch. I prefer Mcleods myself, the StreePro is what I have, 350 HP holding power, stock pedal feel. Spec also makes very good clutches. I wouldn't really consider anyone else.
Doing it is not too hard. Removing the pilot bearing is probably the biggest pain. I rented a slide hammer from Napa, and used the single finger end.