Caution

I've decided to split the cases and have another crack at it. After many a discussion and opinion from more experienced than I, I've troubleshooted to the best of the collective ability and have realised that the possible causes and the outcome from checking each pose a risk of damaging something on what is a new engine. Unless someone else has a suggestion I'm going down the road of caution.

The facts.

- When putting the flyside bearing bush on the crank, I got half way through tapping it on after heating it when I realised I hadn't chocked the crank webs, Mistake 1

- Pulling the crank through the bearing, clutch side, I was so focused on keeping the home made pulling contraption straight and the pressure off the bearing, I neglected to ensure that the conrod was clear of the case, it was only after realising while turning the nut on the bolt got harder, that I realised the conrod was caught and was most certainly caught with enough pressure to cause the crank to be forced out of true. I undid the nut and hit the crank back enough with a rubber mallet to free the conrod, did this unseat the bearing? I don't know? I just pulled the crank back through until it was home, I should have pulled it right out and checked everything. Mistake 2

-Once installed I noticed a bit of play in the bearing, only a few mm and I was assured that it was normal. I proceeded to put the case halves together, I had a lot of trouble and it seemed to be getting stopped by something. On and off a few times and finally, without really finding anything out of sorts, I got them together by heating the cases and giving them some love with a rubber mallet, only to realise that in my efforts to try and figure out why they wouldn't go together, I forgot to put the kickstart gear back in.....off and on again and then I realised that the crank wouldn't turn without some slight force and a spanner on a nut on the flyside of the crankshaft, I kept turning it and it got a little better, but it was catching on something. Mistake 3

- I split the cases and found that there were small shavings of alloy throughout the crank area, seals etc, the leading edge of the crank web was shaving the smallest amount off the repaired rotary pad. I eventually pulled the crank and  tidied up the pad and the crank web with a dremel and tiny wire wheel, I chamfered the leading edge of the web slightly to avoid it shaving any more. I reinstalled the crank and put the cases together, the crank spun by hand so I though it would be ok. Mistake 4

 I proceeded to finish getting the engine to a point where I could kick it over, to my surprise it did after a while, ran for a few seconds and stopped not to be started again that day, something wasn't right, turned out the retaining clip on the clutch assembly didn't want to play and the clutch fell apart in the case. Since then I have tried everything to get it to rev with throttle applied as explained in previous posts, idles ok for a while, plug fouls with oil,  lots of white smoke, 2% mix, 2.5 turns on the mix screw, timing is fine, carb and jets checked and cleaned, everything is torqued to spec and the only thing I haven't done is actually put the engine in the frame and hook it up in prep to ride it, but I can't see what difference it would make and I'm reluctant to only because the engine in there is running like a dream, reliable and I've learnt over the years that if it ain't broke, don't fix it....the only thing I can think is not quite right is the crank as explained above.
Back to the drawing board for now. Happy for some input guys....