If you're talkng about the wires going into the firewall plug, yes, you can. Any wire that leads to any sensor in the engine bay and that is attached to somethign on the engine must be left intact, save for a few things, please bear with me XD. The ABS sensors, brake system sensors (proportioning valve, etc), airbag sensor, power steering, a/c (I'm MOSTLY sure your Eagle harness will still run the A/C), alternator wiring (unless you wish to reduce the number of "swap codes" that will be present in your engine computer permanently, by using a computer controlled 4.0 alt), fan sensors/relay (another swap code). You can rewire for VSS, fuel pump etc quite easily, and those are the ones cut that lead outside of the engine bay. Make sure you don't forget the oxygen sensor connector (grab the 02 as well, in case it does actually work. Most yards will sell sensors like that for super cheap) and crank sensor/connector. That one is tricky, but best tackled from under the vehicle. Pay attention to the backup light connector as well, though that also depends on what tranny you're going to go with. If you have an intake manifold and throttlebody available, pull those too, they're surprisingly hard to find sometimes. Make sure all threaded holes in the intake manifold have a sensor or vacuum fitting inserted..
Philotomy, your eagle is EFI too? I'd love to see some pics of your setup