is the stutter random or does it follow a pattern when the rpms are at a constant speed, ie idle. Honestly it sounds like a vacume leak in the egr VSV's on top of the valve cover, or the VAF has dead spots in the resister strip. 4crawler has a write up on how to cheak the VAF. Other thing is you could have gotten a o-ring from the top of the injector croked and/or pinched. After that cheak the vaccume advance on your distributor .Put a timing light on and watch what the timing does when it hits the stutter. Do it at idle, hold the throttle up at constant RPM in a few diffrent RPM ranges, and check when you rev up fast and than drop to idle. With out the diag. port shorted the idle should be 5, and timing advance should be around 12-14 when you rev up i think, FSM should have that spec. Also see what happens when you pull the vaccume advance line off.