maybe the pickups/guitar are not as much of a contributor to the feedback problem as you may think
microphonic tubes in your amp may be contributing as well and if you change (or even just switch around) some of the preamp tubes you may greatly reduce the problem
in the OP you stated that you don't have the problem with your strat so that means it must be the PRS but since, using the same logic, you didn't have the problem with the other amp (Marshall?) then maybe the amp is a factor too
consider that the output of the PRS is much greater than that of the strat so the combination of potentially microphonic tubes and high gain pickups may be the issue
you can test your tubes for microphonics by
gently tapping them with a wooden pencil (use the eraser if it has one) and listening for a ringing sound through the speaker - sometimes, if the tubes are really microphonic, you can hear the ring just by tapping on the front panel
Ya, Im not an electrical troubleshooter by any means but I did get a bucketload of new tubes and tried every combo possible using a schematic that states what tube does what channel yaddayadda. After a suggestion to try a different guitar, I plugged in my Deluxe straT with NOISELESS pickups..Wimpy , yes, compared to the PRS...hey, that rhymes:D. Anyhow, the volume level that I can get with the strat is waaaaaaqay more than Id ever need and no feedback of the annoying kind. WE are a fairly loud stage level band but this squeal happens at a fairkly low gain and volume level...shouldnt be there.. I will try the Mesa and the PRS at practise thursday and see. The Mesa is not as wild as the EVH.