Cutting the heads of those "nails" won't hurt anything else. I just wish I was there because I have hundreds of those nails from unused parts in the spring kits. Many kits come with two or three nails of different lengths because they are used with shoes of various widths. At the mileage you listed, it is prudent to replace the return springs, so you will need the hardware kit anyway, but if you do not want to go that route, you might find some nails from a friendly mechanic, especially one at the dealership. I had box full of them in my tool box for this exact reason.
That metal plate you are referring to sounds like a stamped slot. Those are supposed to be pounded out with a hammer and punch, then you put those rubber plugs in later.
Thursday, August 18th, 2016 AT 3:48 PM