Finally got the job finish today and the tyres refitted, they did the old fashioned water bath test and no leaks so far so fingers crossed it's worked first time.
Many thanks to people on here for the advice and suggestions, there obviously isn't one single right way of doing this job as there are many slight variations. I've chosen what I considered the best ideas but I'm not saying this is the the best method by any means but it's work for me.
Cleaned the inside of the rim with acetone, which was actually watered down because it was £1 a bottle nail varnish remover ��, and then with thinners.
Cleaned up the surface where the tape would be applied with a scotch pad wheel on a battery drill, also tidied up the weld on one of the wheels were the tyre would seat against the rim.
There was evidence of water ingress from the spokes on the rim tape, quite a few rust spots, so I decided I wanted to do something to try and seal the spokes and nipples mainly to stop water getting in from the outside underneath the tape. I decided to use what I had to hand already which was some loctite 542 thread sealant, applied it from the inside of the wheel around the nipple and the spoke threads, it's anaerobic so what was left on the surface I had to wipe away but hopefully what's run into the threads has gone off in the absence of air, either way if it's worked or not it won't affect the ability to hold air it was just extra insurance against water leaking in.
Used 3M 4411n 50mm wide tape, originally ordered the 2 mm version but was let down so ended up with this but I think it's plenty thick enough. Even though I had the wheels mounted on the spindle it was still quite tricky to apply the tape and keep it straight, I was so busy concentrating on minimising the creases and bubbles that I didn't notice it wondering off slightly and had to do the rear wheel rim in two pieces. it was even more tricky with the front wheel rim having the really deep valley, maybe 38 mm wide tape would be better on the front but that wouldn't leave you much tape either side of the the spokes.
Used gorilla masking tape over the top of the 3M to protect it during tyre fitting and maybe give an extra insurance layer, trimmed the edges so they were clear of anywhere the tire was seating.
After sending back my original valves because of the poor quality I ordered these bike-it 90-degree valves and they were much better, a good wide stepped seal which seats the valve centrally in the hole and the nut was a much better fit on the stem then I ones I originally had.
Decided to file a flat surface on the wheels to give the valve the best chance of sealing, finished it with a couple of coats of clear lacquer just to protect the bare aluminium, I know a lot of people would be worried about filing their wheels but you can't see it once the valves are fitted.
I didn't see the point of overlapping the tape at the valve and I'm glad I didn't because with the thickness of the alloy wheel rim on the Thruxton it doesn't leave much of the valve stem to fit a nut, also put a tiny bit of mastic underneath the nut and some PTFE tape around the thread as an extra extra insurance policy. ��
Overall not a particularly difficult job, applying the 3M tape and keeping it straight was a hardest bit, would have been better if I have planned it and ordered all the materials in advance instead of doing it it when I got the puncture, the 3M tape is not that common in the UK.
Even thinking about keeping up small repair kit under the seat with CO2 canisters if anyone has any good suggestions that would fit in the Thruxton seat hump.