Ender 3 Pro + SKR mini E3 1.2 + BLtouch doesn't work with downloaded bin file
A) it tries to exceed the X limits and makes the loud clicking sound while performing the bed leveling. it even tries to move past the X end stop switch.

This tells me that the firmware you use is faulty - it has a faulty bed-size or home.

B)when printing, it moves to the far right rear corner and extrudes off of the bed.

This can be intended in the G-code, or bad homing, again, firmware home position.

C) octoprint can no longer connect with the printer.

This, again is a thing that happens if the firmware is not configured properly or flashed correctly.
You might have accidentally chosen the wrong firmware distribution - your config points to the Ender 3 - SKR Mini E3 v1.2 - BLTouch, not the Ender 3 v1.5 or v2 (slightly different hardware), and possibly adjust the proper homing position.