The final drive ratio within the crankcase is different between a scooter and a buggy. The buggy engine I bought has a 3.07:1 final ratio, scooters are typically 2.11:1 to 2.78:1.
Pic here:
http://www.partsforscooters.com/Vehi...e-Transmission
I could not find a 3:07:1 (13/40) listed in the conventional scooter ratios, so I'm assuming it's specifically for buggies.
So, unless you changed the chain and sprockets, your final drive is too high.