1) I can't get my Jagwire cable housing through for the rear derailleur cable. What housing are you using? Jagwire cables might have larger outer diameters, do you have a standard SRAM or Shimano derailleur cable housing to try? I don't have an IP-106 so I am not sure if you should be cutting the housing and putting a cable ferrule on the end. With my IP-057 I needed to cut the cable and use ferrules, with my IP-036 I ran full housings after figuring out bare cable and ferrules were too small for the openings.
2) Anyone running just the bare cable?
See answer #1.
3) Probably a fairly dumb question but to get the brakes internally routed I am going to have to bleed the brakes aren't I? If you look around, there is a "no-bleed" method of shortening the cable which also applies to running the cable internal, essentially, you squeeze the caliper piston together a bit, cut the cable, then when you push the caliper pistons back out you purge any air that got in the line, and connect the line up to your lever. I have been successful using this method about half the time, then again I was new to the process.
4) What is common stem (and stem size) for this bike, I am 6 ft 1 on a large frame.
Sounds like you would want to start with a 60-70mm stem, but there is no formula for stem length, it's whatever feels comfortable to you. Check your LBS, they may have a set of spare stems you can try which will help you decide. Of course, you will probably want to purchase the length stem you need from them as well.
5) Anyone used the carbon fork on grade 4 / advanced tracks?
No clue here.
