Which 4-stroke engine do you have? As a general ballpark figure, if you set valves to .005" intake and .007" exhaust cold, you should be okay. You can always run a bit tighter or loose if you live in hot climes, but I've found those to work well. My HS49's intake valve was 0.022 the first time I checked it!
All single-cylinder engines have some NVH, that is just because they are inherently imbalanced. For example there is a roughly 800RPM (4200-5000) range in my 4G+SBP setup where there is a harmonic imbalance and it causes a lot of vibration which goes away if I pedal, easy because that's 60-72 pedal RPM for me.
If your setup is always shaking, there may be a problem somewhere that needs addressing.
Can you take pictures of your setup? It would help a lot for all experienced eyes to spot potential issues.