Not Charging after Madd bypass.
One thing not to overlook is to running an equal size ground cable to the alternator, and make sure you have a good ground to the engine block and chassis. I am putting coil on plug ignition with my EFI install and will ground each head too.
There is no reason to pass high amp loads through the bulkhead connectors. I put LED's inside the cabin of the car, move all high amp drawing circuit feeds to a 12V distribution lug under the hood and use relays on any circuit that has an amp draw of more than a handful of amps.