5/3/1 with Knee Problem?

I’ve been having great sucess with size and strength on this program. However I recently tore my minescus a bit in my left knee. I cant tell for sure if it came from heavy lifting or too much running I just know that one day my knee seemed to pop all the time when squating or going up stairs.

I want to continue this program as my Squat and DL are only 3 months from goal but I think maybe its best to give my legs so rest. With that said when I start back lifting should I start at 20-30lbs bellow where I left off? Is it ok to continue with upperbody lifting or will that cause too much of a imbalance? Knee pops pretty loud on SQ and DL but no real bad pain but I think safer is better than sorry.