Sam.

Did you use the IA Reference Picker utility to lookup the necessary info for choosing an appropriate slot and naming the BAM files accordingly, or just dump in something from the EEs?

AVI2MVE which is a command line tool written by ABel.  Most convenient place to grab it is probably with PS GUI, which also provides a GUI front end for it.  There is also an older tool written by (I think) the original developers, but it's 16-bit so doesn't run on modern architectures.  Last OS that could run it was Windows XP; anything newer requires an emulator, but last time I did that was probably on Windows 7.  I think the name of that package was something like "MVE tools".  I can try to dig it up off an old hard drive tonight if you're interested, but it's a pain to use even if you can run it.

Having done a bit of reverse engineering of binary file formats myself lately (the save file format of Baldur's Gate Dark Alliance for the PS2), let me just say that I am super impressed with all you have accomplished.  And the time investment... I wish I had that kind of free time to work on my own pet projects.  Really impressive work!

I gather then than this needs to be installed after EET in order for its files to override the EET versions?

Yes, this mod should be installed after EET.

IIRC, FWIW BAM Resizer was originally designed to scale PST animations down to 75% of original size for use in the BG games.  Coding improvements made since the original release (mostly by me based on feedback from the community) have resulted in options for quality improvements compared to the original release.  I can advise further on its use as needed.