Mark, I've been there!
When I rebuilt my Commando in 2006, having only ridden it for about 6 miles before doing a complete rebuild of everything, I couldn't get it to start. I would kick it and kick it but it would not start. There was a spark on both plugs, the plugs were getting wet indicating fuel getting into the pots, I'd re-check the timing, the compression etc etc, it would pop and kick back a bit. It had Amal MK1.5s on. I was sure that these were the problem as the choke on these are a plunger system similar to Amal MK2s, and so I bought two new carbs.......result? No change.
So in increasing desperation I bought a new Boyer, and it turned out to be a fault on the boyer ignition backplate. I dont know where as I had checked the wires and even resoldered them, but with the new back plate fitted (before fitting the new box) one kick and vvvvrrrrrrooooom the engine fired up immediately :shock: . I was fairly suprised although much relieved.
I know that this isn't much help to you, but if your compression is OK and you are confident that the valve timing is OK, see if you can substitute (preferably from a friend so that you don't have to purchase them) other bits of ignition, and or carbs.
My Commando now has new carbs and ignition, so now I've got over the expense, I'm quite pleased! 8)