We just got done with the b18a swap into a CRX today ourselves. We actually kept the injectors on the Ls and the Si harness hooked up fine. There won't be any wires to add, however when you compare the Ls harness and the Si harness with each other, you'll notice a few extra plugs on the Ls harness. Don't worry about them. Just make sure all the Si plugs go in, and you're set to go. Also, I didn't do the wiring, but my friends did have to make some of the wiring longer or shorter, because not all the wires were the same length on the motors. If you call this modification of the wiring, then yes, it does have to be modified.
Hey, sleeper how'd you go about doing the shift linkage? We ended up cutting the one that was solid mounted on the Si tranny shorter and bolted it to the underbody, since the Ls engine doesn't have that mount. Then cut a section out of the actual shift linkage of the Ls shorter to fit. Is this anything like you did, or is there an easier way?
One more thing....when she bought the motor mount kit there were only 3 mounts. We were like, "wtf?" So we put the engine in leaving the front motor mount bracket in. If you are ABSOLUTELY sure you're going to do the swap, and you are ABSOLUTELY sure that you will never swap engines again, cut the front bracket out, or just bend it down. It is not used, it is a pain in the ass to work around and you don't end up using it. *shrugs* Good luck, and hope this helps