Are you sure it's a simple conversion to vertical exhaust on the 990? I too have the newer style 990 with under-hood exhaust (which I don't care for) and asked my dealer about replacing it with the vertical stack from the older style 990. He looked at the parts lists and the pieces have different numbers all the way back to the manifold. That would mean a new exhaust pipe, muffler, manifold, maybe mounting brackets, etc. He didn't think it was worth pursuing at all. If you find out different, let us know - I want a vertical exhaust!
If it is indeed more than a simple final pipe swap, I'll probably just build my own. The final pipe just bolts on to the muffler so it shouldn't be too hard to bend (or have bent) a different pipe that comes out the side and up. Fab up a flange to weld to the pipe and bolt it on. It would also require cutting a hole in the side panel, but that's no problem.
Actually, now that I think about it, maybe the old style JD pipe could just be modified with a different flange to bolt to the muffler ....