Birge,
It sounds like you pulled the radiator cap and drove a new truck under it!

Describe the stutter or miss. Where do you feel it...steering wheel, seat of your pants, where!
When do you feel it? Under slight load. Can you duplicate it at will.
With all you have done to the engine, It almost sounds like you are feeling a bum u-joint, motor mount or some drivetrain phenomenon.
Stuart