OK, well, some news.
After not achieving any improvements to the misfiring problem, either with Mikuni VM34s or MK1 Amal Concentrics, and after trying a wide range of jets and needle positions, we concluded that the problem could not be a carb issue. So we fitted a pair of stock 79 XS650 Special headers/exhausts (with balance tube removed and plugged) from my chop build donor bike and voila, misfiring all but gone, with Amals fitted. However, the throttle response felt a little sedate. So I replaced them with the VM34s, re-jetted to:
MJ: 180
PJ: 22.5
NJ: 159-P8
JN: 6F9
Got the motor warmed up and took it for a run up the mile long straight outside the workshop. Result: throttle was crisp, pulled well through whole range of throttle and apart from just the slightest of cough on full throttle it was misfire free. Totally transformed. So I think it goes without saying that the 2-1 exhaust was the problem (most likely the collector). Obviously this is a major success, though I shall run it for a few days under varying loading conditions just to be sure, and check out the plugs to see how they're looking, but after just a couple of hard, fast runs along the mile straight today they'd gone from being quite white to quite a nice biscuit brown on the bridge. Early days. I should be happy you're saying. Well, yes and no. Yes, it's great to have a bike that is responding how I would expect, but, I've lost the 2-1 exhaust that was a big part of the street scrambler look that I wanted on the bike. So I either settle for new headers and two reverse mega's (not perfect) or start looking at further experimentation by way of re-fabricating a new collector, this being the likely cause of the problem. So it's, dig out the exhaust design books, churn the calculations and test a few options. At least I've now got a backstop position if I can't get a good 2-1 set up fabricated.
Just like to say thanks to everyone who input into this post. All very helpful comments. Will let you know how I get on with the 2-1 testing.