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Sometime in the future i will need to repower my Mule, It appears the Honda GX390 should be a perfect fit..
anyhow, the original engine (FE290D-DS08) is equipped with a 14.5 amp alternator with 2 charging wires that both go straight to the regulator (6 pin), now my question is, if it a later date i swapped the FE290 for a GX390 Honda (i'm looking at one with a 18 amp alternator) would i be able to re use the old regulator?
The engine (gx390) also comes with a regulator, but i'm not sure if it would be compatible with the UTV, i've attached the buggies wiring diagram. and the GX390 http://www.smallenginewarehouse.com/GX390QNR.html

Looks like it should work with existing regulator. I'd try it. Two ungrounded AC wires from the stator on both units. Probably to a bridge rectifier & regulator so the output voltages should be the same with more amperage available.

Regulators typically do 2 jobs...
1) They stabilize the voltage to around 14VDC so that the battery can be properly charged
2) They limit the normal charging current to around 1A so that the battery isn't "cooked" to death

In order to do this work, they are typically built to withstand much higher demands. I see no reason the old regulator wouldn't work on the new system.