I you only swapped the engine and not the PCM then there should not be a SKIM issue as the existing key and PCM will remain matched. Normally if there is a SKIS issue the SKIS Red led...or "Key" icon on early models....flashes or stays on. If it flashes it means that the chipped key is not recognised and will let you start...it should run for about 20 seconds before cutting out! If the SKIS light stays ON then it means that the PCM did not get acknowlegment that the ASD Relay has energized....due to a blown fuse, Bad ASD Relay or bad wiring.
The SKIM module sits at the top of the steering column with a "loop" going around the ignition key slot to read the chipped key so you can have a look to see if that SKIM module exists.
Assuming the new engine you put in is OK, do you get fuel and a spark? Does fuel pump run?
Maybe your new engine has bad camshaft or crankshaft sensors, a fuse is blown somewhere, ASD and Fuel Pump Relay needs swapping out or a bad connection somewhere.