First off are you shure you are hooking up the alternator wireing correctly?
Things blowing up or burning out is useually a sign of crossed polarity or a dead short in a big wire.
Assumeing all that is correct take a negative battery cable loose and hook up a DVOM meter or a amp meter in between the post and the cable, there should be no voltage/amps shown with the key off. If there is remove 1 fuze at a time until the reading goes away, put the fuze back in after each reading. This will isolate which circuit has the draw. Then trace out the wireing for that circuit, looking for shorts or open circuits, or a device left on.
A lot of work but the quickest method I know of.