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I also had this problem with the end-stop bolt hole. I found it easier to drill holes in the back cheapskate plate and move the belt clamps there so that they no longer interfered. You can see what I did in the crappy cell-phone picture below.

I also have issues with the set screws in my timing pulleys. I think they were tapped to a thread other than M3-.5 because my screws stripped the threads. I'll try retapping them to 6-32 like you did.