XRR lighting help!?

Hey Guys!, I have a 2002 XR650R with the baja designs kit. It was originally my dads bike but has had little attention since moving from California to North Carolina in 2006. I recently started riding it and have had a few problems. So after getting the bike inspected and registered i threw a new battery i had made from a local battery place (interstate battery) thinking it would help my lights from surging and dimming when stopped. I threw the new battery in and it worked that night. The next day i hop on the XRR to go for a ride and it was like riding without a battery. I hooked it up to a volt meter and the battery was reading out around 4-5 volts and the cables were pushing around the same at idle but when under acceleration increased. Im horrible with electronics and would greatly appreciate some tips on figuring out why the battery isn't charging. Do i need to pull the battery out and charge it even if im riding it almost daily? Or is there something im missing? As far as i know it was working fine with the previous battery before it died. I plan to convert all the lights to LED soon but for the mean time would like to have working brake lights and signals as well as a headlight that doesn't look like a dim candle

Like most systems you cannot take out more than you put in....the stator will produce a % of spare juice with nothing else connected in other words running the bike with no lights etc., the coil & CDI both need power yet again a certain % of what is available what's left over is what you can use to run lights etc. and any excess after this can be fed back into your battery to maintain it's charge.....Go back to basics and disconnect or turn off any power sources and run the bike and see if the battery then holds it's charge....

4-5 Volts means the batt is beyond dead, charge it immediately.
Then when full put it back and check the charging voltage, with whatever users On and revving the engine sufficiently (run a hosepipe over the radiator so it keeps cool) - does it charge 14.2Volts over the battery?
If not (which I suspect is the case) then fix that - and yes, ol' Maus is right that you should not / cannot draw more than the stator generates continuously, the battery will obviously drain.

Oh, also check if there's any current drain when the bike's switched off - should be 0 Amp's!