As soon as I put a replacement fuse into the central locking fuse holder it blows. No other electrical issues besides central locking and remote trunk not working. Is there a common place to look at for pinched wires or a component in the system that is a known issue?

 

I don't believe there are any known issues with an unmolested system, however I can think of two mods which could have
introduced problems:
1) if there's an alarm, it normally interfaces with the keyless module for locking/unlocking, and may have been added to the same fuse
2) some people have tapped into the trunk release circuit to supply constant power to the accessory plug in the glovebox, which is notorious
for failure. However, if the plug works when the trunk release fuse is blown, this hasn't been done.

 

No aftermarket alarm and my accessory plug is only powered with ignition, and works fine. The only think out of the ordinary on the interior is LED light strips in the footwells that seem to be powered off ignition, not always on. I guess its possible that the control box has an internal short, I will dig around a little today.

 

Alas I think you'll need to start checking circuits with a multimeter, which will be much easier with an
S2000 Electrical Troubleshooting Manual