A reason to build up a new bike is always a good thing! A few thoughts and tangents for you......
I haven't yet had the opportunity to ride the full GDMBR, but did ride most of the Montana section several years ago. For fun, I did that section on a Reynolds 853 steel 1990s hardtail, 80mm fork, v brakes , 26er x 2.1" tires, 3x8 gearing, etc. The bike performed beautifully, including the brakes. I did have an early version of the Jones cut bar on that bike at the time. Decent bar for that trip, but suboptimal for the few singletrack sections IMO/IME.
Front suspension is a fine choice. When I return to the GDMBR, I will probably use a rigid bike.
You appear set on the Jones bar, that's cool. I've moved on from my Jones bar..it was a good experiment and helped me fine tune what I like, at least when it comes to mtb control style bars. It may handle singletrack better on a Jones bike, or a bike w/ geometry more similar to a Jones than the 2 bikes that I tried it on.
Pedals, no feedback as I ride spd's exclusively for distance and dirt riding.
Wheels/Tires: I have one 650b/27.5 set, Velocity Blunt 35s w/ 52mm actual Rene Herse tires. Fantastic combo. No experience riding plus/ultra wide rubber and corresponding rims.
Gearing: I would go 2x. I loved the 3x8 setup that I used on the Montana section...old school, perhaps, but it just worked and worked better than the trendier gearing setups used by my companions. Now, I really like the 1x setup on my primary hardtail, perfect for undulating single track in the Sierras, which is where I do 90% of my riding on that bike. But I wouldn't want to ride that gearing w/ a load on the GDMBR.
Brakes: I run mechanical discs exclusively on my disc-equipped bikes. Various reasons for that, including that I view hydro setups as "black box" style componentry w/ corresponding upsides and downsides. I also like to build up my own bikes and enjoy fine tuning/perfecting the mechanical side of things. Mechanical discs do reward good setup.
TRP Spyres/Spyke: My "adventure touring" bike came equipped w/ Spyres (which are the drop bar variant of the mtb Spykes). Good overall brakes, but not out of the box IME. I did not care for the stock pads, and noticed immediate and significant improvement w/ basic Shimano pads. Spyres are also sensitive to good cable setup (but housing is less important IME). Use top quality cables like Jagwire pro series or better. Running 160mm Shimano XT rotors. Prefer them to prior experience w/ BB7s.
My favorite disc brake setup is actually the front disc, rear v brake setup on my hardtail. The front disc is a Paul Klamper, rear V is the venerable Avid single digit 7. Ridiculously good braking and modulation w/ Avid SD7 levers. Not advocating a rear v brake setup, of course, but the Klamper is superb. Yes, very pricey, but I view it as a long term investment in a non-disposable bike component. Comes stock w/ great pads, and the easiest install and setup of any disc brake that I've experienced. Also super easy to keep pads in adjustment. But a pair of Klampers might blow your budget...especially now when they are still relatively scarce due to COVID and commanding a premium in used market. But they are the real deal IMO.
You could combine cable/hydro and use something like the recently released mtb variant of the Yokozuna Motoko. A fair amount of positive feedback on the drop bar variants of the motoko and the fancier 4 piston Ultimo. But I still think that brake suffers from black box syndrome. Most folks don't care about that
Rear rack: Nothing but great experience w/ Tubus. If you want something trendy w/ the bikepacking in-crowd, there is the Tumbleweed Mini Pannier rack, which can hold small panniers or cargo cages...which is pretty cool. Sells out frequently.
Frame bags/bags: So many good options now, we are in a golden age of bike bags. I combine bikepacking gear w/ traditional touring gear for optimal setups IMO. I like products from Revelate, Ortlieb, Roadrunner bags and Carradice. For frame bag, I use the top tube Ortlieb frame bag...brilliant because i can easily switch it among various bikes. Don't care for full frame bags. Most important thing w/ these bags is to get optimal fit on your bike frame. One of my favorite bikepacking style bags is my Revelate mountain feedbag and the similar co-pilot stem bag made by Roadrunner (I have the version sold through Velo Orange because I like the coyote color). They look great and are just in the right spot for important things that you want to access while riding or not.
Have fun!
