Welcome to JEEPZ.com. Without the oxygen sensors , the pcm will run the fuel system on a default fuel map. That is why the engine is running rough , it is running rich continuously . To run properly , the pcm needs to know oxygen content in the exhaust to adjust rich or lean which is done something like ten times per second. I understand your build is in the process of near completion but your going to need all the sensors to run the ignition and the fuel system since an injection system is run solely on the PCM. You can get away with that on a carburetored engine but not with injection. O2 and coolant temp sensor readings are crucial ( among other sensor readings) to starting and running from open loop to closed loop ( cold engine to warm engine).
Hang in there and wait until the build is complete before putting any time on that engine without all the sensors installed . I'm sure your doing good so far but would like to see that the build is complete. You don't want to carbonate the combustion chambers and cause a lot of spark knock which is harmful to your Pistons and rods . If the PCM manages to go with the CTS readings and go into closed loop it may run the engine lean before wide open throttle ( rich command open loop ) and increase combustion temperature and pressure and cracking a cylinder head , or worse. Please take the time to do it right. I'm sure it will be worth it.
