[glhonda]

Here is the scenario.
1- 1979 GL1000 has sticky sliders & intermittent running issue -fuel related.

6- after re-assembling the bike runs great the first day.

7 - the next day the #2 cylinder doesn't fire and fouls out the plug
8 - Check the ignition and find #2 wire has worked its' way loose from the coil
-could have been disturbed when I removed & installed the air box..
9 - new plug and bike runs better but not good.

Back to dave's question. Have you checked to see what the timing is doing when it runs bad?
The original carbs had an intermittent fuel related problem, the 1100 carbs have an intermittent fuel related problem? Is it possible it never was fuel, but timing/electronic ignition?