I encountered no issues installing the kit on that bike, Billy, and I am as certain as I can be that the bike was running fine when I left it. I will say that short end cans - particularly without a db killer/baffle - do not give the best results with the Fazer 1000. Not enough back pressure, in basic terms.
You correctly consider the possibility that there might be something else other than carburation which isn't quite right on your bike, or that something might have been altered after I did the Full Monty. I think it unlikely that the previous owner deliberately messed with the carbs, though. Just a thought - I assume you've confirmed that the gearing is stock ... a few owners have lengthened the gearing to improve cruise fuel consumption at the expense of acceleration. I would also look at the fuel filter and resolve the TPS issue when you can.
I have noticed over the course of working on several hundred Fazers that some are smoother and stronger than others. In some cases the differences are very marked. Some bikes bikes brought to me have sounded rough and lumpy and no amount of carb synching after 'Ivanizing' would get them completely smooth. Others were like sewing machines. These are the ones I described as being 'accidentally blueprinted' on the production line. By chance alone, every tolerance and clearance would be near perfect resulting in a strong, almost vibe-free motor. Clearly there are some that would be at the other end of the spectrum.
How the motor was run-in may have been a factor, too. If babied from the outset, bores glaze and the seal between rings and the bores is never properly established. You might have one of those bikes, unfortunately. I know of several owners who have owned two or more Gen 1s and they would tell you that they were able to discern differences between the best and the not so good that they've had.
Sorry I can't be of more help than that.
