So ever since I've owned my MR2 both the engine lid and intercooler fans have never worked. So today I traced the wire and it went from the positive side of the plug of the engine lid fan, to an earth and then to the intercooler fan, so no wonder it isn't working lol.

Obviously it was working at one point in time, but not sure what is missing. Where should the wires go?

Engine lid fan isn't from factory, the factory wiring/fusing to the IC fan doesn't do a good job of running an aftermarket fan let alone two.
A solution would be to run each fan off a fused relay, getting power from a constant power source (fuse box) and using the factory IC wiring to trigger the relays.

Yeah I knew that the engine lid fan wasn't factory. But where is the original intercooler wire?.. Where does it come from?

It goes over the top of the engine at the front. With the o2, cat temp sensors and AC wire

Wouldn't happen to know what colour the wire is? My engine has wires running everywhere lol.

Gen3 is blue and blue/white not sure about Gen2 but maybe the same.
 
There is also a black fan control box next to the ECU

Is the ecu in the boot? I have an aftermarket one, but going by the amount of cut wires in the boot that's where i am guessing it was.

Yep in the boot. The black box is mounted around the center of the fire wall. It has something like fan control unit written on it.

Awesome, thanks.

So the fan control box is not there.. I swear its a nightmare doing anything electrical on my car, no wires are original.