I can answer some of it for you.
The transmission: Don't try to have anyone rebuild it. The best long-term solution is a remanufactured one from Joe at about $3500 installed. The next best is a used Japanese one either off ebay or from a JDM importer. They usually have less than 60K miles on them. They can be had for roughly $500 shipped, uninstalled.
The timing chain itself does not need to be replaced. It's the plastic-backed chain guides that have to be replaced - around $1000 in parts and labor.
The dead fuel pump could actually be a dead Fuel Pump Control Unit (FPCU). There's a way to ground the dead FPCU to see if the Fuel Pump still works.
zerothread?id=195962
In any case, the pump needs to be replaced - maybe both. The fuel pump has to be new and is roughly $350 or so, plus labor. A used FPCU can be had for $50 or so.
Overheating is unlikely to be fuses - more probably just your thermostat. Replace it only with a genuine OEM one and see if that fixes it.
To remedy the deferred maintenance, you should probably flush all fluids - oil, differential, brake, power steering, etc. Once you get it running, you'll want to get the intake path all cleaned up, especially with the current conversion to ethanol in gasoline. First, I'd ohm all the injectors to check them, and then have a BG dealer do their full intake cleaning service for about $150 or so.
Modified by 96Qowner at 11:36 AM 10/5/2006