This is my first time using the tool, so I'm sure I'm doing something obvious, but here's where I am:

I installed Python 2.6
I installed PyFFI

I used BSACMD to extract the Vanilla Oblivion Meshes
I ran PyFFI on all the meshes (took a very LONG time)
(I right clicked on the "meshes" folder and clicked "optimized with PyFFI" so it should have heeded the skip list)
repacked the meshes using BSACMD with no compression

Replaced the original BSA file with the new one containing the PyFFI meshes

Now I go to start up Oblivion and it starts up just fine. But whenever I try to load a save game or start a new game it's an immediate crash to desktop.

Can't figure out what I did wrong.

I'm beginning to think it's something I did with BSACMD

As a test, I took the Vanilla Oblivion Meshes, unpacked them with BSACMD, repacked them with no compression, overwrote the original file, and Oblivion crashed to the desktop in the exact same manner. It seems I'm packing the meshes incorrectly...

There's no need to repack them after you've PyFFI'd them, they'll work just fine if you stick them in your Meshes folder. The main reason why they're in a BSA file to begin with is that it saves space on your hard drive. It's not a requirement though if you can spare the room on your drive. You might even find that the game's a bit faster, since it no longer needs to uncompress the file before using them.

Use OBMM's BSA browser. The instruction for repacking the vanilla pages are on the opening post of my thread (see the second link in my sig.)


Edit: The problem is likely that you the leading white spaces have been truncated on a certain set of files. There is a link to a Bash-mergeable patch in the opening post that should take care of the crashing. It points Oblivion to the "new" files.