I think you have a different issue than I had. My issue was stupidity. I hadn't clearly understood what an isolated ground was at the time and when I had hooked my Gen 2 alt back up, I hadn't properly put the fiber washer in the right spot. DOH! Got it switched around, and many new fusible link replacements later, it works like a charm.
On a side note, something to watch out for is that the replacement alt's being sold at parts stores don't always have the right pulley. The first one I got, was the right part number and everything but had a smaller pulley. I was still able to get it tightened without hitting the stop, but it chewed the crap out of a belt and when I took it back, they got me another Gen 1, same part number mind you, with the correct pulley and all has been good ever since I put that one on.