Timing Issues after CAS replacement

I replaced my CAS and even after setting it to the spot I marked before taking the old one off, the timing is way off. During the swap my battery was disconnected so I don't know if that has something to do with it. Even after going through the whole process of jumping TEN and ground and setting timing set(with the engine idling 850 RPM). I drove it and it was great but after it cooled down for several hours, it started to idle at 1500 RPMs and stumbling off the line. It continued to do that even after it warmed up again. Did setting the timing right after having the battery disconnected have something to do with it? Edit: Its a 93 1.6L