Okay, been there done that with these cars.
First, since you've crossed out all the major likely problems, you're only left with a couple.
-Get a coolant flush..i mean FORCED FLUSH from a machine.
(you may have a clog somewhere in the engine or heater core area.)
-Check your Temp Sensor.
(it's attached to the Lower Intake Manifold, near the front left on the manifold....it's got a wire plug attached to the very top of it, pop that off, the top of the sensor should look like this...." <O ", you need a large socket to take it off....the actual metal sensor that touches the coolant is like a Brass cone shape material....if it's rusted or gunked up, ITS GOTTA BE REPLACED....autozone has em for like $12 or so, it's an entirely new unit, not just the cone, so it's a 1 minute drop-in fix.)
-Make sure your temp gauge INSIDE the dashboard isnt malfuntioning.
(94-98 mustangs are NOTORIOUS for having faulty gauges, mine even has this problem.....it either runs 100+ cold, or 100+ hot....)
So first off, MAKE SURE you're car is actually overheating.
Now HERE'S what I would ACTUALLY bet on.......
1.) Intake Manifold leak
2.) Improper Head Gasket Install
Intake manifolds will DEFINATELY cause overheating.
It can get progressively worse over a long period....sometimes it will go FULL BLOWN in a matter of 1 or 2 days.
And occassionally the leaks WONT get worse, they just heat up to Half-Way.
So take your guess.....
If you have an Upper Manifold leak, this is an EASY fix, takes a couple hours to do....
If you got a Lower Intake Manifold, this is a 1 day(entire day) project....but is still fairly easy
(i've litterally done it almost 5 times myself.)
Improper HeadGasket Install
There is also a notorious problem with IDIOTS installing headgaskets WRONG on these cars too.
The headgaskets on MY car were done atleast Twice, that I know of.
The last time, it was done by me personally.....never had a problem since.
But REMEMBER, Ford UPDATED the torque specs for the 94/95 v6 mustangs in 2000 or 2002....and not alot of people know about it.
(which is ONE of the reasons people STILL blow head gaskets on those cars till this day.)
A simple trip to Ford Dealer and demanding the specs will work.
(they legally have to copy them for you, dont let them fool you!)
Most Haynes Manuals and Chiltons manuals have the INCORRECT torque numbers and bolt patterns!
(TRUST ME, I have all of them, including the updated Ford Shop manual, and it IS different.)
So consider that.....make sure your mechanics are using the NEW NUMBERS!
(if they act like you're full of ****, TAKE YOUR CAR ELSEWHERE, THEY ARE IDIOTS, period.)
Also, make sure you arent re-using head bolts....that's a BIG no-no.
Also use Fel-pro or Ford Steel-lined headgaskets, nothing else.
Now you mentioned something about warped heads?
Warped heads are a BIG problem typically, because the 3.8L v6 mustangs all use Aluminum Cylinder Heads.
The machine shops can only Mill the heads down VERY LITTLE before they wont work.
(i had a NASCAR machine worker do my heads, and they came out good....but generally it's VERY risky to mill down aluminum cylinder heads....especially heads from a 94-98 mustang)
So if the heads are warped....goto a junkyard and snag a pair off of a donor car.
(you can get them from any 89-91 cougar v6 or 94-98 v6 mustang
i believe, even the T-birds share the same platform i believe.)
I have 1 cylinder head from a 89 Cougar, and other cylinder head is from a 95 mustang......i bolted them right on my 94 mustang, and they work GREAT.
(of course i got them soaked in acid and cleaned first....then milled down a tad for higher compression ratio.)
If you got a cracked head, MAKE SURE it's cracked.
Im telling you, you can get cracks that look REAL, but are actually gasket material that is so thin, you barely notice the difference.
(but most cracks occur from the water jacket to the valve area.)
If you have a cracked head, DO NOT attempt to fix it.
Replace it....goto a junkyard get a new head or heads for like $50-150....done deal!