Alan, I discovered the same thing when I installed my shifter. It is a Hurst Indy model. The stock shift lever put the knob in a very awkward location, so I bought a Hurst truck shift lever off of eBay for $10. It curves into a 45 degree angle, towards the dash. It was also about two feet long but I just cut it down and drilled new mounting holes. It now places the shift ball about three inches from the right side of the steering wheel. I drove the car for the first time yesterday (

) and I actually like the shifter location a lot more than I thought I would. It's kind of like the WRC cars you see on Speed; you barely have to move your hand from the wheel to grab a shift. I may heat the lever up and bend it away from the wheel a bit more, mainly to keep from banging my knuckles on the wheel when I engage reverse, but we'll see after I put a few miles on it.
I know what you mean about how the whole shifter assembly sticks up pretty far. I think it will be concealed beneath the shift boot but I haven't gotten to the point of installing my boot yet. I'm sure there's a way to redrill the mounting bracket to lower the assembly, but frankly after having this car taking up space in my garage for 2 1/2 years I just wanted to get it on the road. I'll let you know how it all comes together when I put the tranny tunnel and boot in it.
I ran my fuel line externally. I didn't want to drill big holes in the frame and wanted the fuel lines where I could see them. My fuel cell drains on the driver's side. I ran the line to the crossmember behind the passenger compartment, along it to the rear of the passenger side, then along the bottom of the floor pan to the first crossmember. At that point I made a 90 bend towards the passenger side of the car, tucked the line between the frame and floor, then made another 90 towards the front of the car at the main frame outrigger. I then followed that up to the front of the motor. I used several of those metal mounting straps with rubber grommets, held in with self-tapping screws. The line is out of harm's way, away from any heat sources, and where I can see it. I did end up drilling into the frame when I installed the self-taps but I used silicone around the screws to try and keep moisture out.
The guy I bought my car from obtained a harness from Haywire. It is similar to the ones Painless sells. Each wire is labeled every 12" with the wire's purpose, i.e., "L Front Headlight", etc. The car was partially wired when I bought it so I didn't have much input in things like fuse panel location, although I don't have a problem with the way things were done. He mounted the fuse panel on the vertical surface inside the front of the passenger footwell. It is pretty accessible there and out of the way of things. A long-legged passenger could contact it but it has a rugged cover panel that goes over it so I'm not worried about that. In my quest for lightness I debated and debated and finally mounted my battery on the passenger floor. It is one of those dry-cell Dynabatts that weighs all of 12 pounds or so. The dimensions are only about 8" H x 8" W x 3" D so it hardly takes up any space at all. I ran the ground cable right through the side of the tranny tunnel and connected it to the Muncie, and the positive cable does the same thing and hits the starter, so each cable is only about 12 - 18" long. Between the battery and the short cables the weight savings over a conventional trunk-mounted setup is pretty significant. We'll see how it works over the long run, but so far the Dynabatt has held up well in repeated cranking while getting the motor fired up and tuned.
I just took some pictures yesterday and will post them after getting them developed (my digital camera is ancient so I went the conventional film route for these)--
Keep us posted on your build!
Bob