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update; I wound up replacing the TPS which helped but I started getting a code on the EGR as well as an O2 code on bank 1 second O2 sensor. I pulled the intake plenum and cleaned the idle control as well as the EGR valve and replaced the PCV valve. Now it runs like it should but I still get a code on the O2 sensor so I will check, and or replace, it and I should be done. Idle is back down to normal range now as well. Thanks to anyone who replied and helped. This is the end of this thread and maybe it helps someone else along the way.

Echoing this. Rebooting sucks, especially when the circlips are stubborn and the bearing retainer doesn't want to pop off. It's extremely messy, too. And for whatever reason, the cost of rebuild/boot kits are almost half the cost of a new CV on RockAuto ($25 vs $50). But as adamzan mentioned, OE axles may be worth rebooting.

Imagine 40 hours for a clutch job... The book time to re&re the transmission is something like 10 or 11 hours... Were they machining the flywheel by hand? If you are up for a project you can try and replace the boots yourself, like Slart said it isn't a fun job and is quite messy. But if you want to save those oem axles, probably worth it. The aftermarket ones are OK, and they make some extended travel ones now that would be good if you plan on offroading it or lifting it.

Wow, $2400... that's a bit excessive. I know things are immensely more complicated on more modern vehicles, and the exhaust creates it's own problems because it's in the way, but ya... That's a bit much for anything, except the timing belt on these things. If I were to guess, I would say that they quoted you that much because they didn't want to do the work.