Yep, I can understand that. Nothing worse than sweating over a bunch of cables and then seeing it not boot, with thermal paste all over your hands, clip ties littering the floor, the dog munching on a SATA cable etc.
Like @Franze said, keep the M.2 #1 512GB as your OS drive plus bits, stick a 2TB in the back (just check MSI are all good with that extra $300 warranty thing if it needs some deconstruction to get at the back of the board like that first though). The spinny drive with the SATA connection in that bay you can use as a door stop and replace it with a 7200. I would be tempted to leave it a bit though, as maybe you’ll just Ortho it up and it will be good enough?