Man, that's frustrating! I'm sorry you're having all these issues with it. It should flash straight on top without any issues. I've done it probably about 5 times over the past 3 days when I was testing builds and never got a hang on the boot animation. I'm sorry to say this, but if it didn't work on 2.0.0, I don't think it will work on 2.0.1 because I didn't change anything with the apps. This update is all script updates (along with the required files in xbin, etc). But give it a go and you can always go back with the theme uninstaller if it doesn't work.
Yea its strange indeed as I believe PF gave me no issue back on 1.0.8 but ever since it's been a nightmare. I can live without it becuase otherwise, your base ROM has been top notch for me. Looking forward to loading 2.0.1 as I also noticed a bit more battery drain on 2.0.0 although not as severe as others have reported. If dirty flash gives me issue, I'll start over once again from scratch.
PS: what's the ETA on the 2.0.1 utility being avail for download?
Many thanks!