I have a 92 yj with a 4.0 and an ax15. It was recently submerged in water up to the hood. I drained all of the water our of everything and cleaned everything with diesel fuel/transmission fluid mix. It cranks fine when you crank it for the first time. If you park it and crank it up a few minutes later you have to put the gas to the floor for it to crank and you have to hold it on the floor after it cranks for about a minute until it starts running right. It sounds like it is only hitting on a couple cylinders until all of a sudden it springs to life and tachs out. I have changed plugs wires rotor button distributor cap and fuel filter. The computer was throwing codes for tps map sensor oxygen sensor and the coolant temp sensor. I changed all of them and now it is still throwing the codes for the coolant temp sensor and map sensor. I have reached my level of ignorance with it.
Check out the crankshaft position sensor. Water could have messed it up, and I am not positive that it would show up on the codes. Until I replaced mine the engine was all but dead below 1,800 RPM but would come to life above that level. It also caused the starting problems you mention.
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