The surface and edge quality of your splitting body is pretty horrendous.

You might expect quality like this on a final fill-in surface that you have to shoehorn into place and can't come up with another way, but not on a primary or secondary surface. definitely not one you want to use as a tool. This surface needs to be rebuilt from scratch using good technique so it is a clean surface.
It's hard to say exactly how you got here, because I decided not to slog through your time line-

No idea if those errors are related or not. frequently errors in the timeline will cause odd things to fail down the line. As long as there are errors in the timeline your chasing your tail. those get fixed first and a the happen
Also-when making solids and surfaces, there is an order to which tool you give difference to.
Always-
1-extrude/revolve if that achieves the shape
2-sweep if extrude/revolve won't do it
3-loft/patch only if you can't do it another way
You've lofted everything, and it looks to me like most everything could have been done by extruding and trimming.
if you have sketches, diagrams, etc of what you trying to do you can probably get someone to help you.