I get some thumps and creaks from time to time. They come and go depending on temperatures, outside conditions, etc. Not a whole lot you can do unless you can reproduce it with the car in the air. Thumping noise from the rear corners could be from almost any source. Since you just replaced the struts - I'd wait until they settle and see what the noise is like then. Before that - double check that all the bolts are still torqued down. Most of the time, any unusual noise from the suspension, especially after replacing some parts are due to bolts and nuts backing off on their own due to vibration, wrong torque, etc.
As for the POR-15 application, dry and grease free is best. You want to maximize the amount of metal contact with the POR-15. Actually sticks better to freshly wire-brushed rust surfaces, or sandblasted surfaces. Something with some surface roughness to allow the POR-15 to dig into.