After-the-fact debriefing:
I re-booted both front axles today. The passenger-side one 100% from inside the engine bay, driver's side partially from inside the engine bay and partially from underneath.
Instead of buying the (craftman) recommended drive pin punch, I bought a 5 piece kit at harbor freight. With coupons it was $5 or so, and while it doesn't have a perfeclty-fitting size, it worked fine. I bought the clamp pliers somewhere (o'reilly?) for $10, and some aftermarket boot kits from rockauto (I think this is going to bite me in the butt, though). I had the circlip tool from before (harbor freight as well, probably $3 or so).
Anyway... the passenger side was extremely easy to do. I couldn't remove the Y pipe before, so doing this from the top was almost the only way around. Driving the pin out/in wasn't a problem at all, and things came apart/together without a hitch. Grossgary: "extremely messy" is an understatement!!! I went through half a roll of blue paper towels on just this axle! The rings you mentioned were a nuisance but not too bad. I just held the whole trunnion with one hand, removed the circlip with the other, and off it went. I cleaned the rings one by one to avoid mixing them up, followed all the other instructions by the book and was done in probably 1 or 1.5 hrs (I took my time).
Driver's side access from the engine bay is not that easy. I removed the pin from the engine bay and began pulling the axle (Fairtax: pushing the transmission to the opposite side helped a lot!), but it was soon too obvious it was not going to work (steering wheel shaft). I ended up doing things from underneath the car, and it went somewhat smooth, except every time something fell it a) was grease/greasy water and landed on my hair, or

was something that is supposed to stay clean and landed on the dirty floor.
In any case, after a ~$30 investment and a couple of hours of my time, both axles have been re-booted. I have the impression the axles are going to fail sooner than later (apparently the booths have been ripped for a while), but what the heck.
Finally, to answer my own question: Yes, if your engine is out and you need to replace your inner boots, go for it
Edited by jarl, 04 August 2011 - 08:48 PM.
Keyboard is failing :D