91 zephyr 750 only running on #3 and #4 cylinder

Didn't know to post this in this category or carbuerator category but this is my problem. It is only running on cylinder 3 and 4. Just replaced all four spark plugs not to long ago. Have started it on full choke, (obviously by sound alone can tell its only running on two cyl.) and will only run on full choke for a little bit then while still choked it full throttles by its self for a moment then dies. Checked all spark plugs and plug wires are making strong spark. Cylinder 3 and 4 will run when cylinder 1 and 2 spark plugs are taken out and/or when plug wires arent even connected. Cylinder 3 and 4 spark plugs look a bit black but not bad and are obviously igniting fuel and making combustion. Checked Cylinder 1 and 2 spark plugs and they look brand new out of the box, no sign of any type of use, literally. They don't have any carbon or any color change or anything and obviously have not ignited fuel or made combustion once. I did install new main jets, float valves, pilot jets, and jet needles in each carb. Then followed instructions on tuning the pilot jets to a rough tune. When i unscrew the float bowl screw on each carb they all flow fuel fine. What could be the issue? Any help would be awesome. Thanks

I'm a carb guy.  The first thing I do on any old bike purchase is a full and complete carb rebuild.  This involves a full break down the carbs, soak the bodies and jet parts in carb dip, then reassemble with all new O-rings and gaskets.  What you have done is replace a few easily accessible parts in the float bowl.  That is not a carb rebuild, since the carb body internal passages are likely plugged up, and you didn't replace all the O-rings.

Are you sure the plug wires are connected to the correct plugs?

Also, are the jets and such that you replaced factory or aftermarket? Some of the cheap aftermarket stuff creates more problems than it solves.

I did replace needle jets, Orings,  seals, and diaphrams, I checked all the parts i could though and they seemed fine and didn't look clogged or gunked up at all. I should let them sit in some carb dip though thanks for the help.

Yeah plug wires are connected to the right plugs... I used a parts unlimited carb rebuild kit. I don't know if that's a good brand or not. Is it? Rebuild kit didn't cost an arm and a leg but it wasn't cheap either. 

I took the carbs back off and used one of those tools with the different sized wires to clean out any type of hole and all the parts. It's running on all four now. Does anyone know how many turns out I should have the pilot screws? #1&2 are #90 mains, and #3&4 are #92 mains. Thought maybe 2.5 turns out but when i gave it a good twist of the throttle it studders. Before that I was not counting but had them turned pretty far out and it was very responsive, but since I lost count of how many turns on each one I reset them. The Haynes manual says only 1 5/8 turns out but is for the uk model so anyone that can let me know how many turns out I should go I'd appreciate it. Thanks

Strickly about the pilot screws, and this is in my personal case:

The Kawasaki factory manual says the pilot screw should be out 2 1/4, but personally, I found that acceptable only by running pilot jets #38, instead of #35.    

When I had the stock #35 pilots, I had to out about 3 1/2 turns to make it acceptable to me..     Remember, factories lean low rpms, because that's where emission tests happen.

,,,,,,,And for the records, in the US, stock, the mains for 1 & 4 were #88, but running #90 is not a big deal and should not affect anything other than fuel economy.   Factory Pro, which makes jet kits for the Zeph. maintains, that was done because the air intake runners are longer on 1 & 4, than 2 & 3.. 

....oh, and I added a shim under every needle.    But that's was me for what I perceived as flat spot at around 4K rpm..   Again, this affects also fuel economy...my range is only about 130 miles.