If I am reading this correctly, your lights were fine until you switched from gen to Alt, right? I am assuming your alt is a 1-wire and you are not using the regulator that was running with the generator, with the mechanical regulators, you could go in and adjust to get a bit more voltage, some would even run 8 V and put an 8V battery in the vehicle to make the starter spin faster. It may be that your generator/regulator was actually putting out higher voltage than your alternator.
