Yep, sounds like you have a bad infestation of scale. Personally, I would probably start over, It takes time and diligence to get rid of them ALL and it sounds like you have a lot! When you think you have finally gotten rid of them all, in a week they can be back in full force again because you missed some. Easy to do! The ones your seeing are under the brown bump is their protective covering, others could still be in the crawler stage and they are almost transparent and very tiny, they are the ones you can't see. Soapy water, or alcohol mixed with water are a couple ways to try and get rid of them, also, your finger nail could scrape them off as well. The sticky stuff is honeydew they secrete after sucking out the juice from the plants leaves. Nasty critters! Billy Rae

The flowers also turned brown today and some of the upper leaves have turned speckled tan and darker brown. Here's another photo if it helps.

Plant looks great to me. You will always have a few leaves die on you. Looks like it could use more sunlight. Not direct but if indoors, a sunny window. Doesn't have to be but it will give you maximum looks and growth. I would water it more and don't let it set in water. During colder months, cut back on the watering. Sounds like you are doing everything right.

I’ve seen this before! On my crassula “baby necklace”. I ordered it from Leaf and Clay and it came to me that way. Then they started popping up more. I picked them off... never saw them again. But I also sprayed with Bromide neem oil solution after picking them off (it works as an insecticide and fungicide, just to cover all the bases) I have an extensive peperomia collection and never seen the brown dots on any of them, only the crassula. Weird. I would just grab tweezers and pick them off, then spray with your preferred insecticide just in case, and then call it a day unless you see them again. It didn’t seem to hurt my crassula at all and they continued to grow normally during and after the spots.