Alright! Alright! Alright!
1. Contact Waltly, they will help you fill out the necessary numbers. In my case, the most crucial info was the fork length & offset. You can also change the figures as you progress. They will ask for a 50% downpayment before they officially begin with the project planning. Plus the planning stage can take a few weeks.
2. You can just tell them the chainline value you want. While your CAD drawing would help, it is not required. I didn't have that, I just list down the numbers, accompanied by pictures of Niner SIR frame & it's geo-chart. Any numbers I didn't list that they required, they asked. If I don't know, they suggest but I decide. They will come up with the drawing for you to check & approve. And every time you have a revision, the drawings will be updated accordingly.
4. They will inform you if the 40T is doable with respect to your tire size & chainstay length.
3., 5. & 6. I'm afraid I'm not technical or knowledgeable enough to answer these questions.
7. I never asked them but I believe they have a default derailure hanger based on your chosen dropout. They might have options for you to choose. In my case, I was deadset with the sliding dropout with those brackets... so I didn't bother to ask.
8. Top tube mounts for bags aren't a bad idea. It gives you more options for choices of bags (I do see a lots of bolt-on bags on the market nowadays) and mounting strategies. The only hitch I see is bolt-on bags looks/works better on flat top tube. Perhaps you can ask Waltly if they could use oval top tube or offer a square-ish tube. After all, Litespeed Ultimate Gravel Ti Bike is sporting a square-ish top tube.
9. I believe it is worth it. The only reason I didn't have them on my 'Niner SIR' was because I already have a gravel bike with those features. I pretty much already defined their roles. And I believe these added features won't cost too much. It'll probably fit in the basic rate. In fact, I'd go ahead & ask if they can build the rack for that frame.
Suggestions:
1. You could consider your max tire to allow you to slap on a 27.5+ tires. I had consider the idea but having rode a 29+ and extremely loved it, I know I want a dedicate 29+. But just a thought.
2. You might want to tell them if you want polished or brushed or sand blasted (?) finish. While I didn't ask, I have a feeling you can have mixed-finish.
3. If you have pictures of features you like/want, show it to them. They will let you know if it's doable or not. Heck, we took a month of trying to make that 420 chainstay length on a 29+ frame work but we couldn't. What I mean is, they will try to give you what you want. You may not always get it but at least it wasn't without some effort.