Ok... Just a quick update,
I changed the gas out with fresh gas... checked valve clearance and timing again with the same results.
I pulled the airbox back off and sprayed a bit of starter fluid into the carbs and the bike fired right up. So I pulled the carbs again, and tore them apart. Pulled all jets and such and soaked in carb cleaner, the pilots seemed to be clogged before blowing compressed air through them... I ran out of time before being able to put them back on before work this morning, but will throw them back on this evening and post results.
I am still unclear about the Accel. Pump diaphram... mine has only one hole in one of the two ears, But after reading some old posts on here, some posters have actually made a hole in the other ear of the diaphram with good results. I just find it hard to believe that Honda would have made this problem on this many of the accelerator pump diaphrams? But what the hell... I will give it a shot before throwing them back on the bike.
Hopefully I don't get so mad at the airbox this time and throw it across the garage again.
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Thanks for all the help,
Billy/Portland