I'm sure most of you have already done this but try checking / cleaning the battery clamps. I had a bad hesitation under any acceleration in my 95 SE 5spd. I changed the battery b/c it was causing issues and it cleared up for a day or two then started in again.
Come to find out, I had a cracked battery clamp where it connects to the battery post.
Just another thought.
Check all your ground leads too. That'll cause a misfire.
