last fall the old girl was having trouble running without the choke, so this spring I gave it the full treatment.
  Valve adjust-It was due becasue I put 6 thousand miles on last year..
Cleaned carbs
synched carbs
cleaned and checked all plugs
checked all wires for spark
The bike starts right up, but I noticed the 1 and 2 exhausts were cold with it idling
i ran the bike around about 2 miles.  very poor acceleration.  checked when I got back- same to cylinders were very slightly warm, the muffler on that side was cold.  THe  3 and 4 pipes were blazin hot!
What am I missing???  very frustrated.  I noticed that the air filter cover is missing the foam, but I can't beleive that would make that much of a difference.  Not sure were to go next. 
Very suprised I was able to sync the carbs only to find out 2 cylinders were not working  I 'm stumped
I know that sending my carbs to sisf would probably solve my issues but after being unemployed for 8 months I am really strapped for cash, so I thought I would try to get it working for the season on the cheap  my only other real option is to park it for the year

Nearly impossible for this to be an ignition problem but just for kicks and giggles switch out the spark-plugs with 3 & 4 and see what gives.

The reason that you where able to sync the carbs was that all a carb sync does is balance air flow through an air pump it has nothing to do with the flow of liquid fuel. Sounds to me like your not getting any or very little fuel into carbs 1 & 2 in that there could be a bit of debris stuck in the left side of the fuel delivery T that is in the center of the carb bank. Have you tried draining the carb bowls to see if there is any fuel reaching the left side of the engine?

Long distance guess:

Could the spark leads for cylinders 1 and 2 be reversed?

My #4 header wouldn't warm up at idle due to a fuel blockage. This past weekends carb rebuild revealed grayish white powdery deposits at the float needle and seat. Otherwise the carb interiors were quite good. I`d bet on a fuel blockage but I`m likely not as experienced as the other responders. When you cleaned out your carbs did you do a complete (read scary the first time) disassembly, spray cleaning and inspection of EVERY passage and part?

why would i read "scary the first time" can't find it using the search

why would i read "scary the first time" can't find it using the search

 He means that a full disassembly of the carbs could be intimidating the first time you do it.

 Have you cheacked to make sure the #1 and #2 spark plug wires are not reversed?

Gunk in the tank has plugged the carbs after assembly.
You might want to drain the float bowls.

x3 or so, drain the float bowls on that side to make sure they have fuel.

You can buy an inline spark tester at auto parts store for $16 or less, then can move it from plug wire to plug wire to see if you're getting spark when the engine is running.  I just bought one to troubleshoot a Pontiac Grand Prix problem.

Maybe one of your coils didn't get hooked up right or grounded good enough but I think a coil doesn't handle two consecutive cylinders.

Maybe the plug wires/cap connections got damaged during removal.  The wires should be flexible and don't pull on wires to remove caps.

Nope. The C10 uses a wasted spark system. One coil does 1 And 4 and the other does 2 and 3.

plug wires are not switched.  tested both wires with spark tester, they are working.

verified thatt I have fuel in both bowls.  I used the clear tube method and float levels are correct.

is it possible that wires are loosing spark somewhere like maybe not seating all the way down on the spark plugs?

I was also wondering if I missed something in the carbs?

Carbs - about the only thing that comes to mind is the little aluminum jet needle guide that fits into the throat of the carb and should be inserted from the bowl side toward the throat, not from the top.

So you did all these maintenace things at once, then the bike didn't run right afterward?

Dave, if it were mine, before I went any further, I would do a compression check on ALL the cylinders. Pull the tank, remove all the plugs and disconnect the wires (power wires, not plug wires) from the coils. Check them all at the same time. There shouldn't be more than 15% difference between any 2 cylinders. Because they are paired, you may have a blown head gasket between cylinders 1&2.

txfatboy - are you saying to test 2 cylinders at a time or test all 4 at a time?  I'm not quite understanding that.  If so, explain a little more why testing one at a time would not be sufficient.  Thanks.

Sorry for the confusion. I was trying to say test each cylinder, one at a time, but test all 4, not just cylinders 1&2. Hope that clears it up. Hey, the voices told me it sounded ok.... You still want to make sure to pull all 4 spark plugs and leave them out until your done. This will allow the engine to spin over easier and give more consistent results.

Just wondering, did you figure out what was wrong?