What CEL codes are stored ?
The check valve on the fuel pump is prone to failure, leading to a rapid drop in fuel pressure in the fuel rail. With modern oxygenated fuel and the high under-hood temps the Cherokee is known for, vapor lock can happen quickly in the fuel rail. Until the fuel rail refills with cool liquid gasoline, the engine will run rough and possibly misfire. The misfires can generate P0300 series CEL codes. 300 series codes are not fatal and as long as the engine runs properly and you gas MPG is the same as before I would not worry a great deal.
Clean the IAC and TB, add a can of Techron or SeaFoam injector cleaner in the next 2 gas tank fill ups.
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