Sorry Ryan, your kinda close but not there
I replaced my CPS when I did the ol 00' engine swap and I had the same problem.
Its happening because you didnt get the sensor back in place exactly EXACTLY where it should be and you probably didnt use the alignment tool to line up the shaft gear on the cam, or you are not on the correct tooth.
1.) Get the alignment tool (If you have it do it again)
2.) Re-Stab the CPS and try to remember where you had it before, put it exactly as it was angled before.
3.) Make sure the gears mesh perfectly
4.) BUY THE MANUAL AND READ THROUGH THAT!!!

(I have a couple so I can cross ref them.)
The CPS determines when the fuel injectors fire, not the timing so thats where your problems are coming from. Its a bitch to get just right if you havnt done it before but its not as big of a headache as it seems like.
Chances are that your original wasnt bad, but replacing an electrical part is always a good idea in an engine bay.