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To deal with your assumptions of overheating:
did you correctly reinstall all the cooling shields around the engine? Did you remove or alter the cooling fan?
please reset the valves to a more correct setting, a guess is around 0.005"-- you could check with the seller for exact specs and maybe a manual- if you don't have one
the short amount of run time, cold to 2 min, suggests that the scoot might be running lean-the 2 minutes is about enough time for the auto choke to cease operations. rereading what you have done-- increased engine displacement by 50%, and new exhaust (freer breathing??) -- both of which demand more petrol
you did not say whether you had increased the main jet size or decreased the A/F ratio
also, when you installed the new exhaust, did you get a good seal of the pipe flange to head? if not, more petrol required.
might consider reinstalling old exhaust and check changes.
if it is really running lean, that translates to more heat.-- think blowtorch
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