I have a crapload of IGT stuff. I have a couple of Baja's, a couple of the flat burners, the double stove, a few single BBQ boxes, etc. The stuff is scattered between the house, the cabin, and the camper. It's a sickness...
The double stove is typical SP quality. Great burner; nice flame pattern. But it's not my favorite stove. The bottles hang from underneath. The windscreen can't be used in the IGT frame, as you said. And honestly, I rarely, if ever, need two burners. I'll usually take more prep area over another burner.
The Baja is a nice piece of kit. But the folding legs make it heavy, because I don't use the folding legs. But on a frame like yours, the weight probably won't matter, and may in fact help keep it from rattling.
Anymore, when I reach into my stash for a cookstove, I grab a Flat Burner. The only thing I still don't like about it is the grate has these upward pointing horns that limits the size of the pan you can put on it. One of these days I'm gonna cut them off. The Flat Burner fuel knob and canister hang from the IGT rail slot, which is nice if you use canisters, but must be factored in for a build like yours if you don't use the frame. The knob/hose assembly comes with a little bracket that allows it to hang from the burner. It works, but it kind of dangles there; I like things rigidly mounted.
I'm in the early stages of building a fold-down frame for the back of my Sprinter camper that will utilize my IGT stuff, so I can identify with what you're going through. If you want to pay for shipping, I can loan you whatever I have, so you can mess with it...