Hi RCcola55
If you are going to design a replica engine, it would be advisable to keep identical external dimensions and also bolt hole threads and dimensions for the bottom end so accessory parts designed for the current Chinese bicycle engine can still be fitted.
My 2 cents worth,
1) Design the bottom end to use crankcase reed valve induction and eliminate cylinder intake ports.
2) Design the cylinder to use boost ports.
3) If possible, look at the idea of a wet clutch system to improve primary gear life and also to reduce gear noise.
4) Give thought to engineering an electric start (add-on) option.
5) A good point of engineering reference would be the design of any of the current 125cc dirt bike engines (Honda CR125, Yamaha YZ125, Suzuki RM125, Kawasaki KX125).
6) An even better piston option may be to use a piston from any one of the above manufacturers or to use the Husqvarna 3120 piston.
7) Design a correctly balanced and manufactured crankshaft using similar design principles to that of the above manufacturers.
8) Design a method for reduced cranking effort when pedal starting the engine with high compression levels. I've suggested the use of a readily available compression release valve but any engineering solution that achieves this goal would result in a satisfactory outcome.
Cheers Fabian