Here are some thoughts, all non-professional: You'll have to provide a rear compartment inner wall and seal it, just like the regular boiler on base setup, to direct the exhaust down the back of the boiler and into the rear of the base, to be exhausted. Alternately, you might be able to seal the exhaust port on the base and move it into the middle, added section. You're going to have to be aware of your draft situation. I don't know how far down you can pull the smoke into the lower base and still have enough draft to get it out of the unit. Maybe it'll be a piece of cake.
The walls will have to be strong enough to carry the 800 lb. boiler, plus added plumbing. Probably no problem, since you are already familiar with working with steel.
The fire won't be as close to the water jacket, so there may be some loss of heat transfer. Not being an engineer, I don't know that answer, but I believe it won't be a serious issue. You might require an extra tooth of feed than a standard setup. Your water has to be tempered anyway for floor radiant heat.
I have often used a coal boiler fire to heat steel. It works nice.
The only potential problem might be the draft issue, but I would certainly try your invention if it were in my shop.