I finally figured out how to manually hex edit the DLC content. It's a massive PITA, but it's done! All DLC weapons have proper ammo and auto reload disabled. So, the Steam version is finished. I will continue to fiddle with checkpoints, and if I figure anything out, will release an add-on for this mod.
Final GOG version coming ASAP.
I will continue to monitor this page, so please let me know if you find any bugs.