Herb is right. You need to flash (polarize) the generator.
Just run a jumper wire between the "Bat" and "Gen" terminals on the regulator.
(Alternately you can jump from the pos + battery terminal to the terminal on the generator that's labled "A")
Just touch the jumper wire for a second; you should hear a "click" in the generator when you do it.
That's all there is to it.
If you're still using the mechanical voltage regulator I'd suggest changing to a Cycle Electric solid state regulator. The solid state regulator works much better and it's possible for the contacts on the old mechanical regulators to weld together and burn up your battery and wiring. (it doesn't happen often, but it can happen.) Also, often the problem on those mechanical regulators was the ground. Check the nuts that secure it to the bike and make sure there's no corrosion between the regulator and the nut.
The procedure for checking and adjusting the regulator depends on weather you have a Bosch or Delco-Remy regulator and describing the procedure is beyond what I could post here. (it's five pages in the Clymer manual.)
Flash the generator and see if it starts charging. If it doesn't, then get a Clymer manual or factory service manual and a Cycle Electric solid state regulator.(the one that mounts to the end of the generator is best.) http://www.dragspecialties.com/fatbook/7/443/5943772
BTW, those alternator conversions have a tendency to wipe out cam chests on Ironheads. I don't recommend them.