If it's pedal lever clearance that your after don't move the motor, work on the pedals or buy some "dog leg" pedals or heat and bend your pedal levers if the are made of steel. Don't attempt to bend alloy or cast levers they will crack and break.
Some vibration is normal with these 2 stroke motors. Your motor mounts should be tight but if you over tighten you will strip the threads in the engine block.
Make sure your motor drive chain is straight and in line with the rear sprocket, if it's not you will feel some vibration & eventually the chain will break or jump off the sprocket & that's bad. Straight chain lines also allow full power to transfer to the wheel. If your not running wide tires you should be able to run a straight chain line without the chain rubbing on the tire even when using a rag joint wheel to sprocket connection. 2.125" or narrower tires usually work great with motorized kits & cruiser style frames.
A close up photo of the area that you suspect is causing problems really helps forum members answer questions and give advice.
Rick C.