Actually, I think most of those changes are complimentary. With a custom bike you can have a hard fork that has relatively the same geometry as your suspension fork, but to the extent that the touring bike has a lower BB steeper ST and HT, that all sounds fine.

The devil is in the details, not meaning it would be bad, but that the idea of approximation is more part of the rack bike build, not the custom one. You will be dealing with an individual who thinks that measuring parts to the thou is reasonable. Yet we are throwing together a bike that will be a sorta. I think that would probably only grab a serious builder if he could see there was a reason for it.

My bigger concern would be the complexity of rigging the bike so the changes can be made comfortably. That kind of rigging gets old. In many cases you will need duplicate everything, so why not just see it through and get another frame. The reality is, a Nashbar touring frame might be more to your liking than the one you will get through this process, and you could leave all the components that define it installed. If it were me I would want different seat, bars, shifters, brakes (or they have to be recabled every bar change), different pedals, and possibly cranks. That is a ton of rebuilding. There is a point where you can just change tires, but once you take it beyond that...