When coming to a stop after putting the engine out gear (99 2.5l w/ manual trans) the engine begins to race to 3k rpms. If you shift the truck back into gear, the idle sub sides. Note this only happens after the truck has warmed up and is coming to a stop. Otherwise it idles fairly decent. It used to have a p1506 but now with the climate control leak fixed all that it currently had is a p0171

 

4cyl only has the one bank, bank 1
P0171 System too Lean (Bank 1)

O2 sensors need to be replaced every 100k miles or 12 years whichever comes first
They can cause a False Lean when they get too old

Manual transmission vehicles will hold a high idle, 1,000-1,200rpm until speedometer shows under 5MPH, its an emissions requirement
Then idle should drop to about 750-800rpm on a 4cyl engine, if fully warmed up

If you think there is a vacuum leak causing the P0171 or the high idle then there is a simple test for that
Warm up engine, or do the test after driving when you get home
With engine idling unplug the 2 wire connector on the IAC Valve, it will close
Idle should drop to about 600rpm or engine may even stall, either is GOOD, it means no vacuum leak
If idle does not drop then there is a leak

 

Disconnecting the iac drops the idle. But that doesn't explain why the engine wants to Rev up to 3000 when coming to a stop in neutral and then hold it there. If you shift back into first or somethibg the idle becomes considerably normal

 

From the IAC test that means the Computer(PCM) is doing the high idle

Not sure if Ford will update PCM software on a 1999 any more?
"High idle" was the most common software glitch in all Ford computers, not specific to 2.5l or Rangers

You could get an under $20 Bluetooth OBD2 reader to view Live Data
Then see what the computer sees when slowing down with clutch pedal down or trans in Neutral
Could be a sensor that is not sending back correct data, still within correct range so no Code, but computer is doing the wrong thing at that time because of incorrect feedback