Well after months of searching. I still have not figured out this knock, rattle sound.
I have been to transmission shops, tech shops, ford, you name it, and each one blames the other. The trans people say its my motor, The tech shops say its transmission, and ford just doesn't know or want to find out.
I have put on it 3200 miles since I purchased it, and it has knocked the entire time. Some days it is more frequent than others.
I changed the oil and I didn't see any metal floating around. I didn't have it tested, but I would figure after 3000 miles of it I should see something.
After the oil change no difference was made with the noise.
I also changed out all the lash adjusters 16. Pretty easy except wiggling the driver valve cover around the booster.
I was very surprised in how clean everything is in the motor. All the valves looked good, no build up or carbon. No discoloration or anything.
I am just at a loss.

Look on the bright side: if the tranny goes, the rebuilder should be able to install the anti-rattle clip (which is the very first thing you remove after the pump is taken off), and mystery could be solved.
This car dates back to just about the time the TSB's came out about this noise. One thing to note is that if it is the trans, then the noise should only happen in O/D. If it happens in second (when the int. clutch is applied), it's NOT the trans.
Just something to keep in mind. I'd run this until it blows myself. Sloth has never been one of my shortcommings, and I couldn't possilbly countanance any reason to take apart my car for a minor noise.
I just work on my junk when it doesn't run.

My plan is to just drive it. I feel its in the torque converter, but thats just guessing. I have no plan to do anything major till I have a more solid clue on what is going on. I would figure a rattle or knock like that would have bombed something at this point. 3300 miles so far. And shows no signs of changing, so its whatever. I just wish I knew. The noise happens in all the gears. I was told at one of the transmission shops I went to that I had a DTC for TC lockup, but wasn't sure if that was just something that came about with the KOEO test. And the other day in the morning, while it was cold, till the car came up to temp on the highway, the TC wouldn't fully lock up. So thats my hopes and dreams. Cause I love the motor. And the car. But at this point I have decided to buy another to make a nice car. If I figure it out I will let everyone know

I know this is an old thread but I am having the EXACT same symptoms in my 03 Mach 1 Mustang DOHC 4.6. And it’s a manual trans. Did you ever figure this issue out????? I replaced the Hydraulic valve lash adjusters in the cylinder I was suspecting. No change. Scoped the cylinder, and it all looks fine. Scoped the bottom end through the oil pan thinking I might find a loose rod bolt or something... looks fine. I dont know what’s going on? I also did a compression check thinking maybe a bent valve, or valve seat fell out, and the compression check was fine