[Rob]

Chuck
Please refresh my memory, was your engine dyno tuned with the webers? Have you dyno tuned it since assembled?

Your engine is similar to mine if memory serves correct. So, would seem logical they they would be fundamentally similar in carb set up. For ref. my config is as follows:
mains: 175
Idle jets: 55
Imulsion: F11
Air Correct: 180
Venturi: 40mm

With out knowing the answer to Q #1 above, it seems that with the jets you have listed your idle would be fat and main lean. If you idle is fat, you could be putting out the flame in the cylinders in question. I had this issue with mine with the 65 idles (150 mains at that time). If I could get it running well enough to push into the high RPM circuit it would clear out. With this config I was fouling at idle, popping off at (below the low to mid circuit transition ~2K rpms), and most importantly ran way lean in the high circuit (hence the clearing out the rich situation). So, I was running from super rich at idle to super lean above 3K. After a couple dyno runs and "dial ins", the cliff notes are I dropped the idles to 55, raised the main to 175 and adjusted the idle mixture screw to dial out the lean popping. Note, with the 65 idles, the idle mixture screws didn't really seem to have any affect (sounds similar to your issue).

My 0.02