I am just curious. With your anticipated riding conditions, why front suspension, suspension seat post and such wide tires? The suspension element will add both cost and weight to your build. I ride crushed stone and gravel rail trails quite a bit and ride 35 mm tires and no suspension anything.

What I would do if I were you would be to seek out a bike that comes as close as possible to what you want and modify the few things you need to. Just select a couple that look promising based on the geometry information from the manufacturer websites, and that way you will know which bikes/sizes are likely to meet your needs.

The reason I would go that way is that you would probably spend more money going piece by piece than if you can find a bike that has most of what you need.

Since you state no descents, I assume few climbs as well, so I would give serious thought to a single chain ring, or a double. I wouldn't avoid a bike with a triple, but I wouldn't seek it out unless you do some climbing. This would save weight on the crank (and RD, where you could use a shorter cage).

For Shimano components, I think almost anything would do, but I have a slight bias toward groups that are named, and not just low numbers such as C-101 etc... i.e. Altus, Acera, Sora etc, should serve you well.

Sticking to the mountain groups does give a wider range of possible flat bar shifters.