Thank you for this. The ball joints, I believe, are fixed to the lower control arms, correct? I just had the lower control arms replaced and the Shelby 1" drop applied. I did have a ball joint boot that was split but I'm pretty sure, again, all this was replaced with the new lower control arms.
I'll check them out though as I had a mechanic do the actual work about 10 months ago.
Each front wheel has an upper and lower ball joint. Your lower ball joints were replaced with the control arms, but what about the upper ball joints? Those are attached to the upper control arms. Could be the upper ball joints were OK when you had the upper control arms lowered, but now the ball joints are going bad. You don't know until you check.
If your Mustang front suspension is suspect, meaning you don't know what components have been replaced at what time, I would politely suggest rebuilding it. You've already replaced the lower control arms. Cool. Now replace the upper control arms/ball joints, inner tie rod ends, outer tie rod ends, idler arm and shock absorbers. Then you'll know the front suspension is safe and you can drive your Mustang and enjoy it.
If you want to go a little further, you can install roller springs perches. Those are somewhat expensive, but well worth it. Also, I have Bilstein shocks on my Mustang and they are amazing. Don't forget the steering box. Those get worn and make the steering sloppy. You can rebuild a steering box. I sent my old, worn out steering box to Dan at Chockostang and he sent me a nice, rebuilt steering box.