You may be able to get boots by themselves from Energy Suspension, they make nice polyurethane boots that won't tear like the stock ones. If you're replacing all the stuff, the parts should come with the boots.
I just messaged you back (finally haha). By the looks of the work you've done so far, I have no doubt that you would be able to make up your own exhaust for the 4.0 head. It just takes a little bit of patience and ingenuity.