A common issue with motor swaps is that some part of the ignition system can be slightly different, especially the crank and cam position sensors. Make sure they are the correct parts, and that the wiring is exactly the same too. The connectors should all be checked to see that none of the terminals were accidentally pushed out of the connector housings. Was the transmission replaced? What about the crankshaft sensor?
Verify that where the cam sensor mounts to the engine, and any sensor wheel on the cam is exactly the same as the one of the 1999 engine. Verify all engine grounds are properly connected and none are loose. I have to say, man made problems are the hardest to solve, so good luck!
THE MOTOE CAME OUT OF A 2002 BUT WE CHANGED IT ALL OVER FROM THE 1999 SO WE ONLY USED THE HEADS AND BLOCK I HAVE GONE OVER THE CONECTIONS SEEMS LIKE A HUNDRED TIMES AND THE ONLY TROULBE CODES ARE P0353 COIL #3 AND THATS IT I HAVE CLEARED ALL CODES AND TRIED TO START IT AND IT CAME BACK
interchange on the engine might show the same but with one little problem. exciter wheel on lh cam gear. pull the cam sensor out and rotate the engine, count the spaces in the wheel. should be 3,2,1, or 3,1,2 if they are different than you must change the cam gear. crank sensor will be the same,