We bought an MT once that had your symptoms. We tried all sorts of things to make it run correctly but we were never successful.. It all made sense when we finally pulled the head to find that there was a fairly large hole in the font piston but the missing part was nowhere to be found..... Detonation appeared to be the cause of the problem. Hopefully yours is a easier fix.
I'd do a compression test to see what you have then I would pull the tappet cover to see what might be causing the problem. Many times an engine that sits for long periods of time gets a sticky valve which bends a pushrod/breaks or bends a rocker. The valve lash likely needs setting anyways.