Dude,
I've done the same swap in my 85 CJ7 and had trouble firing it up also. What I found was the Jeep used a resistor wire going to the coil. I used a HEI ignition on the 250 and this was cutting the voltage down to the HEI.
I just removed the resistor wire and replaced it with normal wire and it started.
Other things I had troube with were I had 2 plug wires swapped around, the fuel pump was bad, and the timing was way off. I think I finally got it running with 4 deg advance but with the HEI I now run about 10 and have the plug gaps at 60.
This was good swap for me. I've ran my CJ every day for about 2 years with this motor.
Hope this helps
Gregg