CFL2 frame? Is this the one you're talking about?
That one is made for a standard Evo engine. SHould be able to accommodate an alternator Shovel as well.
The frame below is the CFL1:
That one can accomodate an Evo or alternator Shovel without modifications. It can be made take anything from a Knucklehead, Panhead or generator Shovel if you clearance the downtubes.
Most CFL2's were built with 6-speed gearboxes, but should be able to take 5-speed as well. The CFL1's were also 6 or 5, but there have been a few older-style builds that took a 4-speed.