I just bought my 3 a couple of years ago. I've done a handful of mods to it since. I like what your attempting, but I think I'll keep it simple. Even though my 3 is being built as an expidition vehicle, and could benifit from the gear ratios of a 6l80e, a 4 speed is a well proven setup. One of the biggest problems us 3 owners have is the lack of aftermarket support. Your 6 speed will be pretty awesome and unique when it's done, but I'll stick with whatever has the best aftermarket support.
Keep it up though! Any kind of mods for the H3 that are being developed is great for all of us. Maybe one day the aftermarket will notice us H3 owners.
It's pretty typical to run into issues like these when tackling something that hasn't really ever been done before. I think that once I can get everything ironed out, it'll be a viable option for those not wanting to stick with the 4L60e (for whatever reason).
After doing some more research on the TCM problem that I ran into, I can say that if you find a 2009 and lower 6L80e, you shouldn't have the bricking issue that I ran into. If all you can find is 2010+ transmissions, then just plan on swapping in the new valvebody/tcm before you install the trans into your vehicle.
I believe that the 6L80e will prove to be reliable.
As far as the aftermarket for H3s....well, you're looking at it. The guys on this forum are probably the only ones that will be making parts from here on out!