I agree with Faster. Most likely you still have a fuel problem.
Probably several problems all at once. Makes it very frustrating to figure out, so take your time and think. Diesels are actually easy to get/keep running. You need a good battery (or two) and a good starter to spin the engine over fast enough. Second - the glow plug circuit has to be working. Third - fuel
0. If you have even the smallest air leak in the lines it will run like that. Could even be that one of the injectors is leaking internally. Or you are losing prime to the fuel pump. If there is an air leak before the injector pump and it sits for awhile the fuel will drain back to the tank and when you try to run it has just enough to make it cough then dies. I had this problem on a 6.2 GMC, took me a month and a half to figure it out. I had to prime every day.
1. The electric fuel pump could be giving trouble. If the fuel pump has vanes it will not work if even the smallest piece of trash gets caught in one of the vanes. I know - don't ask. ok - stranded on a lake for hours waiting on someone to come by and tow me back. The local marina that was open didn't even have a tow boat service.
2. Algae that was still in the fuel lines clogged the electric fuel pump or the injector pump.
3. Injector pump weak. Could have enough pressure to spray, but not enough to work correctly. It is possible the injector pump does not have enough pressure to open the rebuilt injectors correctly. Depends on how old it is and if it has ever been rebuilt.
4. Timing. I found this site about timing the MD6A
5. You bled all the fuel out already?
I know a good shop if you need any parts or anything rebuilt. (In-laws)