I had a bad bushing on a lover control arm and when I was trying to remove it and I ripped off a ball joint. I had to replace it too obviously. Now, I got another problem: when I accelerate the car has vibration at 40 mph. It goes away at lower or higher speed. It vibrates only at hard acceleration at 3000 rpm. If I accelerate slow, I don't feel anything. What it can be? I have some thoughts. When I was removing a knuckle, it was only hanging on an axle and a front strut. I had to apply substantial amount of force to remove a nut. If I damaged the front strut, can it cause that kind of vibration I got? Or I need wheel alignment? Any thoughts?

You need an alignment so start with that. How did the sway bar link bushings look ?

I got to replace a control arm on the other side as well, bushing there is half torn and after that I will go for alignment. I'll check sway bar bushing. I am thinking maybe I should replace front struts, just in case too. I have original struts with 150k miles on it.

What about your sway bar links

What's you're describing is a classic axle vibration issue. It's possible that worn or damaged bushings masked it but generally it will happen regardless. I've found that oem axles rarely cause this, but many remans or new aftermarket ones will cause this acceleration vibration.

Yeap, it was an axle. Thanks everyone for help.