Motorcycles generally have a single or two cylinder engines with 2 stroke or 4 stroke configuration. The two stroke engines are rugged but not environmental friendly so 4 stroke are more popular. Most of the engines are air cooled to keep the apparatus light weight and simple. To design an engine you can first study the existing engines, then decide your objective and finally you can modify any of the existing designs as per your objectives. Designing an engine from the scratch would be a lengthy process. In designing a power pack, you have to go through stroke selection, fuel selection, lubrication system, cooling system, transmission matching, combustion chamber design, valve train design, engine tribology, exhaust gases and NOx analysis, engine seals and appropriate materials for each engine component.
For example following paper only deals with visco-elastic effects in lubricating oil.
Conference Paper Modeling Low-Viscosity 1st Compression Ring EHL at Large Rad...
500 cc means you have decided the volume of the cylinder and the output range as well. You may start from designing the suitable piston, cylinder and cylinder head as well as combustion chamber design and valve mechanism etc. Be careful that for higher power, you are selecting a bigger sized cylinder but whether air cooling would be sufficient for that or not ?
For the flow and combustion characteristics, "Design and Simulation of Four-Stroke Engines" by Gordon P. Blair, published by SAE. Blair also has similar books on 2-strokes, for Example "The Basic Design of Two-Stroke Engines". His approach is straight forward, and not overly complicated. But he doesn't go into the mechanical aspects.
I started reading design and simulation of 4 stroke engine ... which are the other books will be helpful from material point of view .. as i am want to do P.hD in this field