So I figured I'd post an update in case anyone else happens to have the same problem. Since one person already has, it's probably likely.
After using the UPS as a surge protector for the past 8 years and having my computer turn off after every little power flicker, I figured it was finally time to fix it.

After a quick google search, I was able to find the schematic for this exact UPS complete with proper component designators and values. I don't know if I just previously did not look, or if the schematic has been uploaded since I worked on it last time. I will attach the schematic in case anyone else needs it.
The 5th page of the schematic is conveniently labelled "Battery Charger Circuit". It didn't take long to trace the cause of the blown F3 fuse to a shorted MOSFET Q40. The part number of the MOSFET is 94-2358 which is some discontinued International Rectifier FET with no datasheet available. Since the schematic lists it as a 100V FET and the circuit runs through a 2A fuse, it shouldn't be too critical what replacement is used. I ended up using a 230V 25A FET that I had lying around from a salvaged plasma Y-Sus board. I'm sure this is overkill but it was handy and it had the correct footprint.
After replacing the MOSFET and the fuse, the unit now charges my batteries just fine. I am using two large batteries from a mobility scooter and they seem to be working well.
Hopefully this can help someone else out.
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