The PCM uses the crank sensor to take a sample of the normal crankshaft speed and identify the location of the marks used on the flexplate/flywheel. The sample picture is taken on a hard deceleration event after a battery disconnect or the PCM is reset. It then uses this picture as a reference to the actual rotation of the engine during idle and to a certain RPM. Later model vehicles can detect a misfire over the entire RPM range of the engine, our XJs aren't that sophisticated so the cutoff RPM for detection is slightly lower. When the engine misfires, the amount of time it takes for 2 complete revolutions is different than when the engine is running on all 6 cylinders. The PCM can detect this difference in time/speed and uses this information to set a misfire fault code.
So, with that in mind, the PCM will detect anything that throwns off the crankshaft speed even slightly and will cause a misfire code to set. I have seen a fan clutch that only had 1 bolt holding it on set a multiple misfire code. Fixed the fan and the code went away.
A good compression test will normally tell you if there is a engine problem, swapping injectors and spark plugs will help isolate the problem. If the misfire follows the parts, then replace the parts and try again.