Perkins is a pile of shit.
JD is a decent engine, but JD as a company is shit. Parts are shit these days.
If you want to keep it working forever a 4B/4BT with a Bosch (NOT LUCAS!!!) fuel system will never, ever disappoint you.
That said, I can't fathom putting that much work into a machine that age. I have only worked my little skidsteer a small bit (Mustang 2040), but a good friend works on these things for a living. He hates Bobcat machines with a passion and claims they are the worst designed equipment of all of them. I know he had an old big one in there with a Perkins recently and it was a huge money pit. Always breaking, tons of labor to fix simple shit.
If I were in your shoes I think I'd try to sell it for whatever I could get and look for a better, new machine. Several of my friends have Case 1845 machines with high flow and a 4BT Cummins. They weigh about 10K lbs and will do some serious work, probably about the limit of what a skidsteer can do without getting into TSL territory. If you wanted an old, simple, larger machine that you can work on easily and run forever I'd probably get one of those.