Motorcycle Repair: CHARGING SYSTEM, kuryakin hypercharger, starter solenoid

Question
I own a 95 FLSTF and have had some starting issues in the last couple of months.  Only mods are Kuryakin hypercharger and Vance and Hines long shots w/baffles).  No rejetting as of yet.  The bike was very hard to start and seemed to have a dead battery.  When starting I would get the clicking like a dead battery.  Sometimes the bike would just turnover like it was not getting spark, then I would get a bang and the bike would start.  The bang was not a backfire bang - more like something metal. (This all started happening after I had the bike jumped from a previous dead battery - from a car - big mistake)  I bought a new battery, charged it and had the same problems.  I rebuilt the starter solenoid and checked the starter for grounds - no problems.  I pulled off the primary, removed the clutch, chain, stator and rotor and inspected the jackshaft.  I inspected the stator and rotor and noticed a lot of magnet medal in the rotor and there were some scuffs on the stator brushes.  There is also a 30amp relay riveted onto the rear fender where the voltage regulator etc...attached to. Could that be bad?  My main question is, I want to upgrade my charging system to more amperage and I am not sure of there is any other changes that I need to make besides a new voltage regulator, rotor and stator.  Do I have to change any wires since the output will be higher - or will the new voltage regulator control the output?  I have not purchased anything for my bike. Any ideas?

Answer
First, as to your starting problem. There are several parts in the starting system. The battery, wiring, starter switch, starter relay, breakers, starter solenoid and starter.
Since you put in a new battery and rebuild the starter solenoid, we can probably eliminate them.  Get the bike started and with a volt meter check at the battery to make sure you have a charge. You should be running, at 2000RPM, around 13.5 volts. Make sure you have a good connection at the batery on both posts as well as the connectin to the startor and a good ground at the startor. If that doenst solve the problem I would eplace the starter relay and the main breaker.
All you have to do to upgrade your charging system is but the kit with the rotor, stator and voltage regulator in it. The wires you have will do fine since they are only running 12 volts still.
Good luck and happy riding
Mike