Man, 109k isn't very many miles for the transmission to go bad. Did you change the fluid regularly? Was it burned or anything?
Regardless, i would do the second option. In my experience, a rebuilt transmission is on borrowed time before it goes bad again. Rebuilds seem to last right around 2 years which is just after the typical warranty. Just make sure that your mechanic changes out the transmission filter when putting the transmission in as well as flushing the transmission lines going to and from it. Also, he needs to completely change out all the fluid, not just a drain and refill. I can't remember how much it is, but it's A LOT of fluid.
As far as the other stuff, it is easier to fix with everything off, but 109k on the suspension is nothing. I wouldn't change anything. If the rubber bushings are out on the end links (Stable link kit in your post), you can get new polyurethane bushings from autozone for around $10 and never have to change them again (and they're red, so it adds around 6 HP

).
The right front axle can be diagnosed visually. Are either of the boots bad thus flinging grease all over the place? Does the axle make a "clicking" noise when cornering? If neither of these things are true, don't worry about it, though, that one is a HUGE pain to get off.
Personally, I would go for the transmission and call it a day unless the axle really does need to be changed out.
Good luck, man