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Update - I took the carbs off and cleaned them again and re-installed them. I also took the right exhaust off to see if I could get it repaired as the muffler had several large holes and the severly corroded insides were falling out. Several motorcycle shops advised me to just replace the entire exhaust system with a Mac 4 into 1. I went ahead and order it and installed it. I am disappointed in the quality of the Mac. It took me 3 tries before I thought that it was tight enough to not leak. I started the bike then had to shut it off and fix the exhaust leaks. I did that twice before I had the leaks stopped. and one of the exhaust leaks was the No 1 cylinder.
So now the 1, 3, and 4 cylinders are firing, just the 2 cylinder is not. So it looks like it was a carb issue. The float bowls were filling with fuel but the carbs weren't getting fuel into the cylinders. My cleaning consisted of spraying carb cleaner, running a wire through the passages, then spraying air throughout. It looks like the 2 carb still needs work. Will try again.

Check your valve adjustments.
Steve

I checked the valve clearances quite a while ago before starting my re-build and replaced 5 shims. However since that was the first time I have checked valve clearances I thought I should re-check them so I did and they are all within tolerance.
I am re-cleaning the no 2 carb and the only thing I am not sure about is the outlet (I think it is an air outlet) from the no 2 carb see the picture below. I am unsure how to take the black tube off the plastic fitting to check that it is clear. It looks to me like I have to take the carbs apart to check that the air outlet is clear. I am not sure what the air outlet does or if it could affect the carb, Any Suggestions on an easy way to check the air outlet?

That's a vent for the two carbs. Spray some carb cleaner and watch if it comes out in the float bowl. Sometimes critters can get in there.
Steve

Steve
Thanks for the help. Success finally all 4 cylinders are firing. I tipped the carbs and sprayed in carb cleaner into the air outlet until it overflowed and let it sit, then used compressor to blow every thing out, had to do it a second time and finally got carb cleaner and air coming out the float bowl outlet. I put the carbs back on started it up and success all the exhaust pipes got hot.
Now I have to try and sync the carbs.