cranks but won't start?

When you swapped the engine in, did you have to remove or loosen the distributor at all? There is a cam-crank sync that has to be done if you do, and it won't start or in some cases may start after a really long crank. Also the asd relay will kick on only after the PCM sees cranking rpm, so it wouldn't fire injectors if it is cranking slow or another sensor issue.