Check Engine Light On

Two days ago I got my Jeep (1996 XJ, 4.0L, Auto, 4x4) to run again. Found that it had a bad distrubitor that caused the camshaft position sensor to get worn out. Anyway, now a day later my check engine light is on. Checking the trouble codes, I am getting codes 11 and 12. 12 means that I have disconnected the batery within the last fifty cycles, and 11 indicates a problem with my crankshaft position sensor.
The odd thing is that my jeep still runs fine, and whaile trying to figure out why it wasn't running last week I also replaced the crankshaft position sensor. Any ideas as to why this is occuring???

I believe that the CPS only helps control the fuel injection...It does not control the ignition (the Distributor does), so the jeep can run even with a bad Crank Position Sensor or a bad connection.

Not sure though...It's been a long time since I did one of those?

John