Had the same happen to me. The vanes in the IP are stuck. Also the fuel collar is stuck inside pump. Likely the old fuel turned to gum. You MIGHT be able to get it free if you fill the pump with a good diesel fuel system cleaner and let it sit for a few days. Other than that you will have to take the IP apart and clean it up. Change all the seals while doing that. As for the miss.... well it can be the pump, bad injector (sticking) or likely the valves are not sealing good due to corrosion on the seats and face from sitting.
any luck?