You really need to put the original ECU back in. To read codes, find the two-way connector on left side under the seat, near the rear, and jumper it, or find a mating connector and put a switch in your jumper so you can conveniently use it when you need to. Follow the service manual procedure to read the codes, correct the issue and clear them. Again, with the original ECU.
As for your initial problem of no fuel pump running, time to check all the connections of regulator/stator, clean them up, and especially at the starter relay. Check all fuses are good... what do you see first with ignition on and bike in neutral?