My 99 4.0 auto has an intermittent starting issue. Engine cranks will not fire up. Engine code is security system. Sometimes it will start, just never know when it won’t. How do I fix this?
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You should start your own thread, you should only post in someone else's thread if you are answering their question, just makes it simpler to find answers that way

Welcome to the forum

1999 was first year Ranger V6's got PATS(passive anti-theft system), this means it has "transponder" keys, and PATS reads that key when you turn on the vehicle
If the number inside the key matches 1 of the 3 keys vehicle came with when new, then you can start the engine, if no match or bad read then No Start

This is NOT an alarm system, just a No Start system, its "passive"

There is a THEFT LIGHT on the dash, it flashes every 5 to 10 seconds when key is off
When you turn key on THEFT light should come on and then go OFF, if the Key was accepted
If THEFT lights starts to flash rapidly then Key failed the test, and No start

You need the EXACT security code to see why key failed, there are 6 to 12 different ones, each means something different

For now test you battery voltage BEFORE starting the vehicle in the morning, or any time after it has sat for 6 or more hours
Needs for be 12.3volts or higher
If lower battery is too old and voltage drops too low when starting so resets PATS and No Start
Low battery is the most common issue
Next is failing Transceiver, but code will tell you it thats the problem

So, the battery is almost brand new, very intermittent starting problems. My son drives this truck, and he has been stuck for 30 minutes waiting for it to start. Eventually it does start, but this is very frustrating. Is it possible to bypass the system? If I take it to the dealership, I’ll probably get a repair bill equal to the KBB.

 

It's been reported here that the PATS system cannot be bypassed.
That your vehicle starts intermittently suggests the PATS system isn't involved and that you have some other problem(s).

How many miles on your vehicle? Fuel filter original? Fuel pressure adequate? Failing crank positioning sensor?

 

Fuel filter is brand new, 119,000 miles, fuel pressure measurement is above my qualifications. Thank you.

 

It the THEFT light on the dash flashing rapidly when there is a No Start?