I just installed the JBA's about 2 weeks ago. While I wouldn't call the installation "easy", I think "straightforward" is a good description.
Unlike some of the others, I had several clearance problems. I decided to keep the 65 style "stud" motor mounts, though I had purchased a set of the newer mounts in case I needed them. I didn't really see how the other mounts would have helped. A couple problems I found with the JBA's:
1. The spark plug in the #7 cylinder is a PIA. I had to buy a comletely new tool to get it tight, and almost had to fab my own.
2. The other plugs are not easy, but are at least possible.
3. I previously had straight boot plug wires. There are a couple places where the 90 degree boots are needed (cylinders 7 and 8)
4. Usually the clearance problem is with the steering box. I have about 1/4". But my clearance to the shock tower is less than 1/16". Occasionally, when the engine is cold and idling rough, the header bangs up against the shock tower. Using the other mounts wouldn't have helped very much. BTW, I replaced the rubber mounts while I was at it, and now is the time to do it. The battery cable from the solenoid to starter too.
In all, these problems are likely to be encountered with any decision you make. I had the same problems that you did with my long tubes scraping on everything, especially speed bumps. That made shorties a must for me. JBA's by FAR have the best build quality of any header I have ever seen. I installed mine using Fel Pro performance gaskets, and Stage 8 header bolts (get the longer ones). Don't confuse these with grade 8 bolts, Stage 8 is the brand name.
In all, after I got the exhaust work done, I'm very happy with my choice. But, I can't say that I would look forward to doing the install again.