So here is the fun update to this story. A week after dropping the bike off, they still don't contact me. I call them to ask what is going on and get told "sorry, but we won't be working on it for a few months..." Essentially the same thing everybody else told me, so I took my bike back, brought it home, and I am setting up to do the damn work myself. In the meantime I am just riding it and not using 6th gear, which is more than fine considering how tall that gear is anyway (really only useable above 70+). No long highway trips for now, but I don't have any planned.
I gave it a nice wash and full detail this weekend.
Anyway, I am currently cleaning out my garage, tossing a bunch of junk, putting in some shelving and building a work table to set the motor on and tear it down.
On positive out of this whole mess is that another VFR1200 owner had the same thing happen to his bike and he gave me some wonderful insight into doing the job. The heads do not have to come off in order to split the cases, but instead it can be done by splitting the case and backing out one bolt at the same time. That will save a ton of time and money. I am still looking at about $500 in parts between the gaskets, gears, and a shift fork, but it beats the $2000-3000 repair bill of somebody else doing it.
Since I now have some extra money on hand I may do a few extra things while the bike is apart. I have wanted to de-cat the bike for a while, so I will likely do that and then have the whole exhaust ceramic coated. I may change to a different muffler from the current Coffman's shorty, especially if I do decide to de-cat. This will also require a re-reflash of my ECU, luckily Guhl only charges $100 for this instead of the $350 it first cost me. It should also unlock about another 20hp if I raise the rev limiter in conjunction with the de-cat, giving a total of around 180-185whp.
I am also debating ordering an aftermarket fairing set in a different color. Not that I don't like the orange. I just want to keep the OEM panels as pristine as possible. I am thinking of black, which would match my panniers. Besides, if I ever get bored with one color, it would only take an hour lol.