Sorry, Kelly.
First, is there some type of list around showing certain mods that need it and certain mods that don't? I recall somewhere a small list somewhere but I didn't mark it and can't find it for the life of me. Thomas Kaira has a great list and there are fantastic forum topics on the ESP Cleaning phenom. Anything like that around?
No list like that exists at this time, unfortunately. Best to play this one by ear. The general rule is that all the gurus here run their meshes through PyFFI before redistributing them. When in doubt, always PyFFI. Usually the authors will also specifically tell you if the meshes are PyFFI optimized, so if there is nothing about this mentioned in the mod description or they are not an established guru on these forums, send the meshes through.
#2. Is it worthwhile to run an optimized set of meshes through the process again under the newer versions of PYFFI? My best example here would be QTP III Optimized Meshes. A great mesh replacement when it came out, but that was a while back. Any advantage to running QTP III Redemized meshes through the system anyhow? And would you use the Original meshes or the already optimized ones? My guess here is original, but that's just a guess.
I would recommend you start over from scratch, as although there will be a small benefit from PyFFIing meshes that are already PyFFI'd, any errors that a previous version might have placed into those meshes will be carried over. By starting over with the unoptimized meshes, you will ensure the best results with minimal errors.
C). I'm currently using the PyFFI Optimization Kit v7 and it's IN/OUT functions with the most current version of PYFFI 2.1.9 Stable. It seemed to work great with the Original Oblivion - Meshes BSA. Am I more confident than I should be? Should I push forward into armor and even FAR lod directories? Or should I pause, get myself a Jack Daniels and think about maybe fearing the PYFFI more than I do?
Might be best to pose this question in the PyFFI Optimization kit thread. You can find it linked in the OP.
Finally (a bit off topic I think)... After PYFFIing and recreating the Oblivion Mesh BSA, I remembered back reading somewhere where uncompressed BSAs are the way to go. Is that the case still? Should I attack them all? I'm going to assume that textures and meshes are where I will get the biggest bang for my buck, but I'm not 100% on that.
Loading the BSA uncompressed will mean the game does not need to decompress the resources inside on runtime anymore, which helps minimize stuttering. So yes, this is still the way to go.