I'd almost bet it's the tune since you've covered your mechanical bases for the most part.
I had a misfire that was totally random, but it happend after the car warmed up and while driving around. I got a brand new ford coil (accel has a replacment now, which I found after ordering from Bill J) and magnecore wires AND running an extra ground to the coil, and it solved it (250 miles without one CEL ::knock on wood::)
Is the misfire in any specific cylinder? My raptor would tell me which cylinder misfired, I'm not sure if the xcal does.
