There are two blank lines, EMC may not like them.
I have a few “//” prefacing drill cycles, They are block deletes. EMC may only want a single “/” (slash). See if that helps. Or just remove them. I go through the program first with the // in and block delete enabled, which then just does a move to 0.00" (surface of stock). with a small center drill set to just below the surface of the stock at 0.0", the “drill” lines (N10060 - N10310 for example) thus center drill first. Then I turn off the block delete enable, switch to the appropriate drill bit, and run the section again. The M01 statements pause the program for me. The three sections of drilling are arranged biggest first. I first center drill all three, then drill all three with the smallest bit .089" (labeled as endmill), then just two sections with a .0935" drill, then just one section with a .125" drill bit. sounds complicated, but it’s not. I just restart the program and run the drill sections multiple time to get them center drilled first, and then progressively drilled until all are drilled. No tool comp.
I haven’t ran EMC for a long time, as I run STEP4, the CNC controller program that I wrote.
On mechanical alignment, you will want to adjust the tensioning nuts on the drive screws (leadscrews) that tension the bearings. Also for the follower nut, if it has any. Otherwise, you’ll get backlash. Don’t assume that the software will “take all the backlash out”.
Ask questions on the CCED or my SherlineCNC list. Many more “ears” there…
Alan KM6VV