Thanks again for the comments. I shall pull it to bits and see what the damage is. I was doing about 70mph at the time and stopped in about 500 yards. Initially there was some movement when I kicked it, but it got stuck, so my thoughts are that I may have been lucky and it has not wrecked anything too badly.
As much as I would love the 300cc kit, it is just way to expensive. I reckon with a replate and top end rebuild I can do the repair for a few hundred quid, so £1200 for the 300cc kit seems a bit excessive. The more I think about the bike the mor i believe it was on it's way out anyway. I took it to the dyno because it was bit wooley at the top end and they found the fueling to be fine and no ignition issues. The bottom cylinder leaked a bit of coolant from the base gasket as well, so maybe it has had a few issues. Seems a bit of a coincidence that the pipes had changed as well, but I had only covered 2-3 miles since changing them.
I will continue to request your help, as these engines are pretty new to me.