This is one of those difficult ones to sort out.
My advice would be to re-check everything you have done, don't touch any other setting until you are happy with things you could have changed.
On the basis that the engine ran [albeit for only 45 mins], there couldn't have been much wrong with it - so therefore whatever the problem now is, it must be related to whatever you have done recently. If you adjust other settings before you have found the problem, you wont know where you are.
Re-reading your post, it seems that apart from the ignition timing, all you have done is check and set the valve clearances, you haven't touched valve timing have you? If you are happy with valve settings, it must be a problem with ignition timing, are you sure its set correctly? Go back to basics, things like making sure you know that the engine rotation is clockwise from the RH side of the bike, therefore BTDC is TDC rotated anti clock - things like that. Apologies if you know all this, but people have been known to make those mistakes. get a manual if you dont have one and follow it to the letter.
Check other basic things without changing settings, do the plugs get wet from petrol after a few kicks? You should try new plugs, check the HT leads and pick ups, get rid of resistor caps if you have them etc. good luck, let us know how you get on.
Andy