Hi Nick
It would seem this is not an uncommon problem with re-builds. I wouldn't pretend to have all the answers, ( though I do share your problem), but my research has uncovered some interesting comments which you may choose to explore.
I experienced precisely the same 'run, stutter and cut' scenario' on my first start-up. I would have been convinced it was a fuelling problem. My tank was running low, I knew the carb needed re-sleeving or replacing, she was running very rich and I could not correct that.
But after she stuttered to a stop, I checked the plugs ( a new set) to find them quite black and sooty, but more painfully - without a spark, even after cleaning !
I then discovered that I was running the wrong plug ( a box came with the bike e so I assumed they were OK ) --- They were suppressed plugs, and I was using suppressed caps. Either can weaken, but BOTH certainly will, kill the spark (I'm told).
However, with plugs and caps removed I find no hint of a spark between lead-end and cylinder head.
I'm running a B.Bransden ignition, so was most surprised to find this, I'm in the process of getting it checked-out.
In your case Nick, the finger of suspicion could be pointed toward another factor: Previous posts have suggest that inlet tract obstruction,particularly along the base of the tract where the atomised fuel flows, can destroy atomisation, cause apparent enrichment, and destroy plugs through irreversible contamination. (Efinol fuels being contributory.) -- So check for steps at the flange, a mm. or less can be problematic. ! Engines like ours,and modern (new) unglazed insulator tips are not happy 'bedfellows' --- It seems !
The advice, ----- get lots of plugs and keep changing them or run a 'used' plug, (more tolerant) while you're fixing the other problems.
Not my wisdoms I hasten, but all sound plausible.
Happy days
Flash' (Pete)