Is this the mod you are talking about?There is a check valve inside the petcock for the vacuum line. You should be able to determine if it works by sucking and blowing air through it. All bets are off if you can blow air freely both ways.
I've had some success rebuilding these petcocks. You have to align the holes on the diaphram, to the hole in the block that fits between the two sides of the diaphram, to the breather hole on the main part of the petcock that goes to the front of the diaphram. I learned through trial and error, but the one thing I was overlooking because it's hard to see is that hole on the petcock, it's about in the 2 o'clock position as you look at the front of the petcock, close to the upper right hand mounting plate that attaches to the back plate, close to one of the 4 back plate mounting screws. If that hole is clogged your petcock will not breathe and allow your diaphram to open and close normally.
Also that 4 hole rubber seal under the selector lever has got to be good, as does the seat the little O ring mates to on the diaphram. Your vacuum line should be in about the 10 o'clock position as you look at the front of the petcock. Any little dirt can cause it to fail, I soaked mine in gasoline and put it together loosely, to allow the diaphram to find it's own center and tightened down the screws evenly.
The carbs flooding to me is normal if the bike sits and has gas going to the carbs. Both my bikes have done it when I left it in Prime, and it is clearly stated in the owners manual that can happen.
Also, there is an old post I have been trying to find that I have not been able to locate. It concerns a "modification" to the petcock that will not allow fuel to flow, but you can't forget to not turn it off. I didn't want to suggest that yet for fear of taking responsibility for it should that fail, so I'm still looking for that post.
http://www.thegsresources.com/_forum/showthread.php?t=130786&highlight=petcock+modification