The issue happens because InventoryFilter relied on the strict order of options in [HotKeys] section. It's fixed in 2.0.3:
https://www.nma-fallout.com/resources/inventory-filter-mod-english-version.142/
Might be better to update the installation instruction with editing mods_order.txt.
Also, no need to use that old sfall_dev.zip because now there's a new sfall release (just make sure to tell people not to overwrite the existing ddraw.ini).
The process giving the starting loadout is fixed. Now it correctly gives bonus items based on your tagged skills, as you are not supposed to receive extra stuff from other skills.
You can write your own barter formula script using gl_z_fo1barter.ssl as the base.
If you're aiming at Pentium MMX, at least you need to replace those CMOVcc instructions in sfall, as they are only available starting from Pentium Pro/II.
But even with them replaced, you might still be caught off guard by VS codegen.