Could be a number of things - worn or chewed camshaft; bent pushrod. If you've got good compression, and fueling and electrics have been given the once over; i'd suspect a valvetrain related problem.
You say you've been over the electrics - you obviously have spark at all 4 plugs and timing isn't 180 degrees out?
Engines missing is usually an ignition problem unless something more sinister is at play...