Yeah, I'd replace that "dust cover". They do start to tear, especially when you work on it, like especially if you replace the bearing and as you are done putting it back in and rotating that stupid driveshaft nut (almost done with job) - then it tears
Since you know the shaft has been out recently and you have vibration I would take it to a driveshaft shop. They can check it and balance it, then you'll be sure about it as long as you own the car. I would leave the u-joint alone. In my book, u-joints rank at the top of the list for most often,unnecessarily replaced parts on a car. I've been guilty of it myself.
