A first test would be to try the hood on the engine. If it looks hopeful set the engine on the tractor and retry the fit.
If it don't maybe stick the twin that came with the 12.5/40 into the JD 111(2) since it was already butchered to take one. Just need to fix the leaking carb.
The hood is wide enough but there is not quite enough head room under it. It maybe possible to raise the hood in the front and/or back to make it work. Need pictures. But this is a go so long as I don't have to make any permant mods to the tractor. Would be nice just to have it moving.
For nowall this engine needs for now is some carb work. I am not sure if I will do that with it mounted on the tractor or move it to the test table.