OK, couple things.
1) According to my search on the Chrysler computer, the CPS sensor part number is 04638128, list price $78.25. My dealership sells parts above the factory suggested retail price, usually at a 100% markup. Cost on the sensor is around $48, so expect somewhere close to $100. The part is the same for the 91-92 XJ/MJ and doesn't designate MT or AT. It will fit both trans types, according to Chrysler.
2) To check for spark, disconnect the wire from the ignition coil to the distributor cap and place the wire near, but not directly on (leave a gap for the spark to jump, maybe 1/4 inch) a really good ground source (like the engine block or engine mount bracket). Now have someone crank the engine and you watch for the spark to jump the gap. If you have no spark, then you may have a bad CPS or ignition coil. If you have spark, then reconnect the coil wire and then pull a spark plug wire and recheck for spark from the plug wire, this will check your cap and rotor for direct shorts to ground. So if you have spark going into the distibutor cap, but not coming out, it is the cap and rotor.
3) To check for a bad ignition coil. You will need a basic 12v test light. Connect the test light to the ground terminal of the battery and then check to make sure the light works by touching the positive battery terminal with the probe tip. Now, disconnect the 2 wire connector at the ignition coil. One of the 2 wires will have 12v with the key on, check this while turning the key to the on position. The other wire will be the ground signal from the computer to make the coil spark. So with you test light, verify which wire has the 12volts. Now, move the ground wire from the test light to the positive battery terminal so you can check the ground signal. While someone cranks the engine, check the other wire for a pulsing ground signal. The test light should blink on and off if the signal is good. This test will verify proper operation of your CPS, the engine controller and the wires going to the coil. If all this is good, then change the ignition coil.
This may sound complicated, but it is exactly what a good mechanic will do when you have your car towed into the repair shop. I still bank on the fact that the CPS is bad. If it was the ignition coil or cap and rotor, the fuel pump would run anytime you cranked the engine. You verified the fuel pump works when you turn the key on, so I would say the pump is good. Max posted about the pump wiring havind 2 circuits, he is correct on the older models, but not sure about the 91+ Chrysler injection models. This might be a problem, but is not as likely as a bad CPS.
Long post to say the parts guys might be mixing up the part numbers for the YJ with the XJ which is very likely. The YJ CPS does differentiate between AT and MT, but not the XJ/MJ.
Hope all this rambling helps. Good luck.
Bryan