I've been playing for 13 years and have the exact same problem.... I can't figure it out for the life of me. Well that isn't entirely true, I can do pull offs under "normal" circumstances, but the part I struggle on is if I have to pull off to an open string. For example ACDC's "Thunderstruck". That intro is hard to not get the high E string to sound too. I mute it with a finger on my plucking hand, but that type of pull off is what gets me.

If I am pulling off onto another note, then I simply lay the finger that I will be landing on down across the higher strings to mute them. For example:

Constant pull offs from 5-3-5-3-5-3-5-3. Since your finger is on the 3rd fret, angle it so that it mutes the higher strings (higher in pitch not direction of course). That way you can give the pull off the attack that it needs without worrying about hitting another string. If you do, it will be muted anyways.

But pulling off to an open string 5-0-5-0-5-0-5-0, there is no finger to lay down since you are using it to pull off. Before you note that you have free fingers to use to mute the strings on your fretting hand, that becomes less effective when you are trying to do that in the middle of a fast run. Or even if it is only one quick pull off of 5-0. Can't seem to mute it right.