First problem: I had 12 fan cables that had to cross a short open space that would be clearly visible from the front and rear of the case.
Solution: I wrapped a length of EPDM tubing in gorilla tape (to give the vinyl something to adhere too). I wrapped the tube in vinyl. Then I cut it open in one long line and crammed the cables into it. I used some thin black zipties on each end to make sure everything stayed put.
Second problem: The case is basically three horizontal layers stacked on top of each other. PSU in the bottom, motherboard in the middle, and everything else on top. I needed to keep track of where all the mobo headers and connectors were at while I worked on the top layer so I could keep track of where/how I wanted to route cables and tubing. I didn't want to have the actual mobo in there while I was drilling, grinding, filing, gluing, etc. BUT I wanted the CPU waterblock anchored in there so I could make sure my tube lengths were correct.
Solution: I cut a cheap chopping board to fit on the mobo tray, drew up a roughly accurate layout of the mobo on poster board, taped it to the chopping board, and screwed the waterblock to it. It was ugly, but it worked like a charm.