I own 2001 V6. About 3 months ago i had an issue where my ball joint failed while i was driving and the whole wheel came off. Got it fixed at the shop. I should have got the noise checked out before but i rarely drive the car anymore because i use my work truck. I use the mustang for errands and on rare occasions a trip out of town.
Here is my problem now. I have started to hear similar knocking noises now. The shop told me my drivers side was fine when they replaced things on the passenger side. I went ahead and replaced the outer tie rod on the driver side myself cause i felt some play in it. Noise went away. Next day noise was back. I know enough to know that I don't have much experience diagnosing suspension problems.
I have had some problems with the steering wheel for a while. It wont snap back to center (don't know if that helps diagnose anything). I've got tomorrow off and want to try and fix this if anyone has any insight. If you need anymore info let me know. Just under 100k miles too.

 

I have never heard of a shop only replacing suspension components on one side without doing the opposite side. Parts wear, if a ball joint on one side goes bad, the opposite side will be bad or well on it's way to failing.
It is VERY important to keep the suspension geometry the same side to side as possible. It doesn't matter what you are replacing, ball joints, tie rods, LCA bushings, brakes, springs, shocks, etc. You always do both sides, always!

Some years of Mustangs have problems with wearing out ball joints prematurely, many more have problems with LCA bushings (quite common). You will also want to check your front sway bar ends, they occasionally break.
If your struts are worn out and leaking fluid, they can bang when you hit bumps.

Just whatever failed parts you find, make sure you replace both sides to keep a reasonably consistent suspension geometry.

 

Did you have the car lined up after putting on the outer tie rod?