How bad were your bearings? Did they cause your wheels to wobble when it was on jack stands? That would seem unusual at 3k.
With 30" tires my bearings have over 11k on them, but I do add grease on brake changes.
The squirrely behavior when you're slowing down is more likely alignment. How did you set it, and what did it measure?
Also, did you start with new shock bushings? Were they tight when you put it together? Popping noises are often due to binding somewhere. When assembling new suspension components, best to get it together with bolts hand-tightened, set it back down on the floor, roll it, bounce it around with your weight, then tighten it up.