PVC pipe works great for conduit and can be routed alot cleaner than
seal tight, or flex, I used it on my build as conduit and for the flood coolant.
You can use male adapters for bulkhead fittings as well.
For the steppers I just used the corrugated wire sheath found at any auto parts store and routed them so the wouldnt touch the bottom of the enclosure , I didnt trust the sheath on the Belden cable, but in hindsight I would just buy cable that has a higher abrasion resistance and not use the corrugated wrap as it holds chips and is hard to clean off.
One suggestion would be to make sure you have a washdown hose in the enclosure if you plan flood coolant, makes cleanup alot easier
As far as the holes, I believe cncfusion kit is using the stock location for the bolts. so you can measure them for a reference, on second thought you might want to wait for the kit if you dont have it yet as IIRC the y mount is not centered. So the relief cut in the spacer might not be centered either.
I have pics of mine and will post them this eve after work, if I can remember where that SD card is LOL
JTCUSTOMS