Did you reinstall the old injectors on the new engine? Assuming so, try running a can of BG44K thru the truck in about half a tank of fuel. Worth doing before you have to take the upper manifold and fuel rail off to get at the injectors, which is the next step after your successful spark check. Check the yellow pages under fuel injection or diesel injection for a shop that leak tests and ultrasound cleans and flow tests injectors. Costs me around $15 each. Several good mail in places for this, too, that others have posted here. There are shops that claim to clean the injectors on the car, and some of those use BG44K, but there's no way to leak test or flow test that way.

One other test. Pinch off fuel return hose, the one coming off the fuel pressure regulator flying saucer thing and going back to the tank, and see if the idle smooths out any. Diagnostic for leaking regulator, which could lower fuel pressure, making the most clogged injector cylinders lean out enough to miss.

Does this happen from cold start to warm idle, or just when it's heated up?