Engine vibrations bad for the frame?

Welcome to the forum. You've found the right place for help and advice.

Vibration is a relative term. What some call, severe, another might say is normal. Some are worse than others but all two stroke, single cylinder engines will vibrate to some extent. Just the nature of the beast.

Is your engine mounted solid to the frame? Adding any resilient material, rubber, tape, old innertubes etc, to the mounts will increase vibration and eventually compromise the mounting fasteners and other parts. A solidly mounted engine will not vibrate as bad as one soft mounted. There are things that can be done to make a more comfortable ride such as soft grips for your handlebars, proper chain tension and alignment and most engines will run better (smoother) after they're fully broke in.
Good luck, ride safe.
Tom

The damage to the frame will be a result of the engine being able to move at the points of contact. If the engine is bolted solidly to the frame, no rubber, then it cannot move, hence, no wear. Yes, paint damage can result and some have wrapped the contact points with electrical tape, just enough to protect the paint, not layers and layers.
As I stated above; the more solid the engine is mounted, the less you'll feel the engine vibrations.
'm not in favor of wood as an engine mounting material. It will compress over time and allow for movement/vibration. Try to get rid of the wood and opt for metal heavy enough to hold the engine securely.
Tom