The only sensible thing to do for the project longer than a couple minutes this to edit in Premiere Pro and do the shots you absolutely must process in After Effects as individual comps. Comps are for creating shots and short sequences. Trying to put 80 or 100 cuts in a single cimp is not only difficult to deal with but changes finding the flow with the music is nearly impossible.
If you want to get real accurate about the whole thing your production needs to start before a single frame is shot. Shooting a bunch of stuff and trying to build something later is a really really bad idea unless there is no other choice. I have done a lot of music projects him more than 45 years in the business and even if you can't draw, just block storyboards will save you a bunch of time.
I hope this helps. You'll be in good shape if you remember that you make shots in a AE and you had it in Premier and you mix sound in Addition.
Thank you for the reply Rick. That is unfortunately what I was afraid of. If you don't mind me asking your opinion on something off topic. I've been using Sony Vegas for about 8 years so I know the software like the back of my hand. I recently subscribed to the Creative Cloud though so obviously with Premier at my finger tips it seems logical to learn the software. There are a few things I like about Vegas, like being able to split a clip, splice through it, stretch or shrink it by holding control, the ability to grab multiple tracks and fade down with a mouse click, etc. etc. The work flow for Premier seems to be much different. Any thoughts on the benefits of overcoming the learning curve/rearranging my current work flow to switch to Premier?
Premier Pro is extremely powerful. Anything you can do in Vegas you can do in Premiere Pro. You will catch on to the UI very quickly.
I always duplicate and cut/split the audio track at the precomp ends and then cut/paste the clips into them for synching. Then I disable the audio tracks of the PCs in the main comp, keeping the original uncut audio track intact. I've gotten weird jumps/skips before, trying to run the audio from within the PCs as my final outputs, so I always make sure that I have an original full length audio track in my main comp. In either case, I rely heavily on markers for synching my animation to audio and often I won't even bother pasting the clips into the PCs, so long as I've got markers set for my cues. Make sure "keep nested comp windows synched" (or whatever the wording is) is checked in preferences, so when you jump between comp windows, your timeline should remain in the right place.