Thanks for the suggestions guys. I'm making a list of things to check.
For starters, here's a few things I've already checked ...
1. Plugs are OK. I've tried swapping them for new ones to no effect.
2. The only gearbox bush I replaced is the 5th gear sleeve. I was wondering if I'd made the clearance a bit tight, but the rear wheel turns over easily by hand. But more more importantly, the problem still exists in top gear, which eliminates the sleeve gear bush as a cause (bush doesn't rotate on the shaft in 5th gear - they're locked together).
3. Bike wheels around easily, so no dragging brakes.
4. All throttle slides are opening fully.
5. Fuel system seems to be flowing freely enough. With a fuel hose disconnected, fuel will piss out of the fuel tap way faster than the engine could possibly use it (with filler cap closed). I let it run for a few minutes to collect a litre or so. There was no drop off in fuel flow, so the tank breather works OK.
6. I haven't put on weight (Thanks Keith

)
7. Engine oil level is OK.
8. Crankcase breather is not blocked.
Things I haven't checked are ...
HT leads, coil earthing or the coils themselves. I don't have a scope to check the operation of the HT system, but I could swap the coils and leads for another set. I have no reason to suspect that they're dodgy though, because there's no misfire.
The engine is not missing, coughing, spluttering, or backfiring. It runs smoothly, but is only making about 40 HP at a guess (about the same power as my 350cc Honda). It's actually quite rideable up to about 5000 rpm and I've done a few hundred km since the rebuild. So it's had fresh fuel through it.
Fuel consumption is poor, so I suspect that fuel is getting in there normally (so carbs and fuel system OK), but the engine is not making good use of the fuel available. That seems to point to ignition or valve timing issues. I'm 100% satisfied that the valve timing is OK. I even printed out the old factory drawings of 4C cam sprockets to onfirm that my timing marks were in the right place. That pretty much leaves me with an ignition timing problem.
I'll try Red's idea of wiping the Ignitech program and reloading it. I'll also try to get a better idea of exactly where it's advancing to with the strobe. Last time I strobed it, I was having problems with my Snap-On strobe light, so I only got brief glimpses when the light chose to work. Just enough to confirm that it was actually advancing, but not steady enough to quantify. The strobe might have a loose connection somewhere.
Hmm ... a thought just occurred. I wonder if the intermittent operation of the strobe light could be due to the ignition system not working as it should. I'll test the strobe on another bike.
Thanks for the ideas.
Cam