Running/starting problem

First order of business I would check the health of the battery charging system. If your battery is charging less than 13.5 volts there could be a problem with your stator or your regulator rectifier or both. If the stator is failing it will burn up your regulator rectifier, if the rectifier is going it will screw up the battery. If your battery is weak it will screw up your sprag clutch and starter solenoid. Your best course of action would be to order a replacement stator with gasket from Rick`s motorsport :

STATOR New OEM Style Aprilia Stator 21_008
GASKET Aprilia Stator Cover Gasket 25_004
If this is the case and your charging system fails testing replace you regulator with a Shindegen 847 from Roadstercycle: Home
This regulator is bigger than the stock Aprilia and works much better. You will need to modify the mounting on the side of the bike to get it to fit. Wire the regulator directly from stator to regulator directly to the battery for the best charging. I went thru this ordeal about 3 months ago and tried to cheap out ... don`t. Each of these components is what you will need. If you skimp ... you`ll be replacing the sprag clutch and starter solenoid as well. If you can turn a wrench and cut and crimp connectors you will be rewarded with a well running RSVR that won`t leave you stranded.