It still may have Codes Pending in the CPU despite the fact it’s not yet turned the CEL.on. I have a 96’ & it’s had DTC’s pending, with no CEL...Plug in and Check, nothing to lose-right? Don’t have a Scantool that can do full Diagnostics, Drive Cycles, PID’s (W/explanatio) -Advanced Sell’s ACTRON’s that can do that & more, buy or Rent..
Did this issue just occur one day at startup, or did it start hesitating one day & became a little more prominent each time it was driven? Can you rev it up smoothly while it’s sitting~ does it hesitate only under a physical load? Need to at least establish when you first noticed the hesitation and what was occurring just before or when it was first noticed...
Try cleaning out your MAF Sensor with CRC TB Cleaner, look for cracked Vacuum lines and other leaks (ESP. TB Vac. line in rear) , weak; inconsistent Alternator output(Bring to Advanced Auto & Test) check it’s Connector & all Wires Terminated upon it- verify grounding is solid- on Alternator to Battery Gnd.to Chassis- CPU- Block,.., Abnormal Battery Voltage, Check CTS output, pull 02 Sensor & Clean; reinstall, check Fuel pressure & Flow, DPFE Sensor, Crank Sensor, Check CPU & other Connectors for High Resistance Connections or moisture- clean/reassemble w/Dielectric Grease. That include most things I’ve seen wreak havoc on that Genre’ of 4.6l GT’s, excluding all but one you’d replaced. Vague, if you have more info, it’s easier to help on this end...
If you run a drive cycle with your Scantool, you should be able to log all of every sensor’s operational Data and values - in the playback after the Test.. Good luck!_