Yes, side covers still fit...
I had them mounted like that before I tore it apart, and the side cover fit perfectly over. They're mounted to a little plate that's recessed about a half inch back into the battery space.
The Bunn components came with two hose sizes, roughly 5/16 and 1/4". I ordered some 3/4" ID from McMaster-Carr and some reducers, I also ordered a bit more tubing length, just cause I wanted to run the valve cover vents back out of the way behind the tranny. I think that's all I needed so far. Always a good chance I'll need to relocate something when I get the brake, clutch and shift linkage all connected.
I've been looking at the main harness, and someone has run the wire to the starter relay external to the 15 pin plug. Are you aware of any reason that should be necessary as long as I'm replacing that plug anyhow?