The fuse box is on the firewall above the headlight hi-beam foot-switch, but the top's power does not run through the box.
I'm confused by your wiring. The top mechanism has one, heavy-gauge black wire that runs from the battery side of the solenoid - thru the firewall - to the top switch. The yellow and red wires (going from memory on colors) then go from the switch to the pump motor (wiring goes under the passenger side sill plate).
The only wire in the engine compartment that relates to the top is the big black wire. I'm unclear what the other wires you mentioned are for.
Of course, if someone re-wired the car in a non-original fashion, nothing I say here will make sense.