My experience has been that it is pretty common with aftermarket pads, missing hardware, worn out hardware or something not installed quite right. One of those springs can do it. Check all the hardware closely. Also see if there is any movement of the pads, they should be relatively snug.
I am sure you opened the bleeder when pushing the pucks(pistions) back in the caliper. Would not cause clunking but can play havoc with the ABS and or master. Wouldn't be one of the pistons especially since you didn't have it before you replaced the pads. You have other issues like pulling or locking up.
Have not had a lot of experience with rust prone cars so do not know if there may be anything related to that issue.
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