If you cut the rear motor mount cross-ways you can make it thinner and drop the motor in the frame. It will help with head and spark plug clearance. However it will reduce the clearance for the carb. It will increase the likely-hood that you will need and offset intake.
I almost always cut the rear motor mount saddle to lower the motor and the center of gravity. Sometimes if you go to far you will run into clearance issues with the pedal chain drive sprocket. Rarely a problem but worth looking at.
How I cut my saddles is squaring them up iin a vice and then use a cutoff disc in a 4" hand grinder and cut it down to a least half the thickness. You could use a hack saw and a file and have the same results
If you are interested I will post a picture of what I am talking about.