OP, it's your camera, not all cameras are purchased for resale but for use, do what you want ....
After removing the shell, I filled the holes with "Liquid Weld" (an epoxy). Aki Asahi provided a cover sans holes. In my case I wanted permanent 50/90mm framelines in this M3. In your case you might only want to take the frameline lever off (not the whole mechanism), since you might want the frame-line mechanism to continue working. You can find a diagram how the M2 frameline lever is assembled in
http://pentax-manuals.com/manuals/service/leica_m2_service.pdf. M4 is identical except for having a different lever.
You can fill lug holes in the same way.
Not sure about the ISO dial - never had it disassembled, you might want to replace the back-door with an M4P door instead.
Roland.