That is a setup i've never come across before but if it works, it works. I'd think about opening up that "duct" to allow smoke to get into the cooking chamber. You could do a reverse flow or for simplicity's sake, drill holes in the duct and there you go. Granted you'd need a fair amount of holes if you used a 1/2" bit or if you had a larger one it'd go quicker. I'd probably just drill the holes and see how she runs then adjust as necessary.
I really don't think you'll have trouble keeping it up to temp even with a small firebox. I have a 24x24x24 firebox on mine and the size of the fire i have going will fit inside your firebox no problem. I'd suggest a grate on the bottom to let air get underneith it though.
As for thermometers, I've had tel-tru's on mine for about 8 years and they still function just fine.