Nick,
I know what you mean about the VA system. I think it looks like a pretty good set up, but not perfect. Here are some ideas that I went with for my install:
I agree that the block-off plate, as designed, looks like crap. Since my project was a frame-off, I welded in the plate and filled it in with bondo to give a smooth firewall appearance.
I also got a couple 90 deg fittings and ran the heater hoses through the firewall instead of through the fan hole.
As can be seen from the first picture above, I found a pre-bent 5/8" hose and used that to come through the firewall and mount the solenoid valve. Much cleaner looking.
I also mounted the drier on the core support instead of the recommended spot on the inner fender. This meant making a couple hose modifications, but again, a cleaner look.
Another thing to be aware of is that the controls can interfere with all that tubing behind the dash. It was a PITA to get everything aligned back there so the sliders weren't obstruct by the tubing. So make sure these have enough room to operate.
I have all my hoses hooked up and tightened and I went through the test procedure for the controller. Next is to get the system charged and see if it works. Not quite there yet.
Good luck with your install and I will chime in again if I think of anything helpful.