If you want an almost plug and play solution then get yourself an adapter harness from apexi to run the evo 6 ecu in the evo 3. The apexi harness doesn't include the obd2 or flash plugs so you will need to solder those in if you want to tune the ECU but if you want to run the stock ECU without tuning then you won't need to modify the harness.
The cheapest solution is to repin your ecu plug but you can also make your own adapter harness from parts available at wreckers for next to nothing if you don't want to repin the original plug, instructions are available all over the net.