Just look to see that nothing's been distorted. No weird corruptions or anything. You'll know if you see it. Architecture is generally safe no matter where it comes from. The QTP3 B&M meshes should come out fine, I optimized mine a long time ago and haven't seen anything out of the ordinary.
There is also a range of about 300-400 for the total number of plugins that can be in your data folder.
BSA files count against this too, and going over the limit can also result in CTDs in addition to the other stuff you mentioned.
CTD on startup (before getting to the main menu) usually indicates a missing master.
Can also be caused in some cases by an outdated Bashed Patch, easy enough to fix by rebuilding it.
When trouble-shooting crashes, remember to try regenerating a fresh Oblivion INI.
When regenerating, make sure that iShadowmapresolution setting is changed, the default of 256 is a known cause of problems.
In the part about resetting BSA timestamps, if you're installing a BSA from a mod, you probably don't want that to be reset since the OBMM function sets every BSA file in your Data folder to the same date. If for some reason a BSA replaces vanilla content, the game will pick from them at random and you may not like the results. The reset function is best used on the stock files after you're done making custom packs out of them.
Folders to avoid:
meshes\effects
meshes\dungeons\misc\fx
meshes\dungeons\misc\triggers
Should also avoid touching any of the landscape waterfall meshes as PyFFI sometimes butchers the transparency information and you end up with ugly waterfalls. Same goes for Texians Animated River meshes. Don't PyFFI those. They come out badly.
The same goes for hair meshes, never ever touch those. The resulting mess is very obvious and very ugly.
Also avoid using PyFFI on any landscape LOD mesh that someone generated using the CS. Which more or less means ONLY do the ones that came with the game. The CS generates new files in a different manner and those sometimes crash PyFFI. Besides, removing 50 verts from a file with 30,000 of them in it won't really matter

BTW, I've had no problems at all from doing the entire weapons folder. Nothing came out screwed up.