If the wire was run directly from the battery to the orange/black wire on the fan, all sensors, fuses and relays were bypassed. The fuse is to protect the wire - if the fuse holder was melted and the fuse not blown, it indicates the wires were trying to carry more amperage than they were capable of, but less than the rating of the fuse.
Which is smarter; a 5 amp fuse protecting a 30 amp wire or a 30 amp fuse protecting a 5 amp wire? You can fuse a 5 amp wire at 30 amps and guess which will burn out first?
It's quite likely the fan motor is damaged. As a wire heats from the current, the voltage drops as the current goes up - the voltage drop will cause the fan motor to run hot and slower than normal.
The original wiring was a fail safe design that was not perfect. If the coolant temperature sending unit failed, the fan would run constantly. If the PO wanted the fan to control the fan with a switch, all he had to do was wire a switch into the sensor wire. Open (turn off) the switch and the fan would come on. Close the switch and the fan would come on when the sensor opened.
My personal opinion would be to put it all back as wired from the factory and make sure all functions as designed, then if you want to be able to turn the fan on manually, install the switch in the sensor wire.
Shop Owner and Mechanic with over 50 years experience