Have you proven that there actually is vacuum at that hose thats sposed to open the ,,,,,,,,,,ON,,,,flow thru it. If you have a vac gauge, it would be good to see what the vac level is there. When I mentioned diaphragm, I was thinking the carb diaphragm, and the question was, ,,,,,,if there was a problem with the carb diaphragm, maybe being out of place or leaking, does that affect the vacuum at that vacuum line that opens the petcock.
Regarding the overflow,,this is a longshot,,, is your temp tank,, at a similar height compared to what the reg tank would be if the carbs were on the bike. I am thinking maybe there is excess headspace here, putting the column of fuel higher than it would be under normal circumstance and putting more fuel weight on the needles and seats. The reason I think headspace could be a problem, is that my gk eleven runs less well with only a quarter tank of gas, if I go fill it up, it seems to run better.
I also have to ask, are the new needles and seats, identical to the old ones visually, because if I am reading this correctly, youre suggesting that the new ones overflow quicker and harder than the old ones. The difference could be the headspace thing, or the WRONG parts if I dare say so.