jdm motor in 97 gst

I put a jdm motor in a 97 gst and when I went to fire it up, it only runs on two cylinders. I did some checking and found that there is no spark on #4 and1 cylinders. when I unplug the cam sensor it fires on 4 and 1 but not on 3 and 2. Has anyone had this problem? any Ideas on what it could be?