1995 Mustang V6 - Cyl #3 Misfire - Help!

I am not familiar with how a leak down test is run. Based upon your compression I would not expect a miss.
Try the test General Karthief just mentioned.

Have you tried to clean the MAF sensor wires? Any air leaks between the MAF and the throttle body?
Disconnect then plug back in the various sensors on the engine and air intake (dirty contacts?). Do the same with the engine computer.

Bent or damaged push rod? If you pull the valve cover, check the cam lift for #3 and compare it to the others.

Spray WD40 on the shaft for the EGR in case it is sticking.

Turn on your lights and heater fan on full.. Make sure you have at least 13.5V at idle. Had low voltage problems in the past causing a rough idle.

Running out of ideas.

The backfiring puzzles me. I would not think 90PSI compression would do this.

I would triple check the entire firing order and separate #3 plug wire from all other plug wires.
Start at the plug and check the position next on the coil. Start at the coil and check the position next at the plug. Make sure your diagram for the coil pack is correct and you are looking at the pack from the correct direction with relation to the input plug. Seen this mixed up before on the 3.8.

Backfiring is often caused by running to lean.

Another thought is put an old fashion (needle type) vacuum/pressure gauge on the intake as close as possible to the intake. Supposedly if you have a bad valve it will oscillate by a couple of inches of vacuum every time the valve opens and closes.

There are vacuum lines under both front fenders which you can not access without removing the inner fenders. The passenger side has lines going to the fuel charcoal canister which are known to have issues. The drivers side is mostly the speed control which you can pinch off under the hood.

Do you notice a skip while idling? If so, try to pinch off lines leading off the engine and see if it changes.

What was the outcome?

Yes. Have pulled the injector and check to see if it’s getting power.

Also make sure your injector o rings are not cracked or worn out. Any codes other then the misfire 303 code?

What is the compression after you replaced the valve?
Did you check the cam lobe when you had it a part?
Did you apply Dykem and lap the valve to verify you have full contact between the valve and the seat all the way around?

Have you swapped the #3 injector with another cylinder’s injector to see if the misfire follows the injector?

Absolutely brotha never assume with ignition parts