Unless the 99 is different than 00 and later 4.7s, there is a Schrader valve on the passenger side portion of the fuel rail between cylinders #4 and #6. Try looking again.
Not all scanners are created equal. Just to be sure that there are no codes, use this DIY method: (1) with the engine off, turn the key On - Off - On - Off - On fairly quickly, (2) after that, any codes present will show up on the odometer display, one after the other. If there aren't any codes or after they have all been displayed, the word "donE" will appear.
Post your results.
You replaced the CMP and CKP after it failed to start, or after the backfiring but before it failed to start?
2001 WJ Limited with Quadra-Drive, Kenne Bell Supercharger, 3-inch Kolak exhaust, Stillen rotors (F/R) and MM pads, Addco sway bars (F/R).