I agree with Mentor58. It's fairly common to find it necessary to replace a cassette after replacing a worn chain. The problem usually presents itself as "skipping" in the gears that you use most. My bet is that a new cassette will solve your skipping problem.
Noises that appear to be coming from the bottom bracket can be hard to pin down. The actual source of the noise can be coming from almost anywhere on the bicycle. The pedal/crankarm and crank/bottom bracket interfaces are common candidates. Some other common culprets are the saddle/seatpost and handlebar/stem/headset interfaces.