Crikey, that's turned into a major saga, I just fitted it (dead easy because I didn't have all those extra bits taking up all the space), think it only took about an hour. Solved the tank prop problem by sticking a piece of wood in there. Plenty of room under the seat and no extra connectors on the battery post.
Because I had a modified pipe (looked standard but had been cut open, some pipes removed then welded back together) and no obvious map available I tried a few maps until I found one that felt best. Then just left it alone and enjoyed the improved performance which was pretty obvious on my older bike, didn't seem any more thirsty either.
In fact I'm now thinking of going back to an FZ6 again as I've had a couple of bikes since and don't enjoy them so much. So more than likely I'll be searching Ebay for an FZ6 Power Commander soon
Glad it all worked out in the end