Just replaced 2.0 DOHC in 98 Neon. Used the alternator from the old engine. It worked fine before but it doesn't charge now. All connections look good to me. Did I miss something?

 

If it worked fine before and now it does not, chances are you missed something. Bring it to autozone and have it tested to make sure, but its unlikely that its bad if it worked before. check for loose or disconnected wires, thats most likely the problem.