As an owner of many PRS guitars, thought I'd chime in here. The rosewood neck on the Modern Eagle's makes them a little finicky with pickups emphasizing the right frequencies.
I had a Custom 24 with a RW neck and was recommended a pair of Rebel Yells. While I loved the definition and clarity, they just weren't what I was looking for in that guitar. I think with RW necks you have to compensate for a loss of some of the lower mids, while also not increasing the lower frequencies as to become too muddy.
Anyhow, I happened to sell that particular Custom 24. For my next RW neck'ed PRS I would def go with something with more mids, and less highs like an Abraxxas in the bridge.
For the neck pickup, I personally like something more vintage, that really lets that certain "woody" tone from the RW neck come through in a nice creamy way - something like the 57/08, but maybe a little more output - Mule or Abraxxas.
FWIW, I currently have a Custom 24 with a maple neck and ebony board that was way too bright and thin when I first got it. So after talking with people on this board I went with a Crawler in the bridge and an Emerald in the beck Couldn't be happier!! Best pickup upgrade I've ever had - totally changed the guitar. The Crawler really has a bark and a roar that works great for rock and hard rock, etc... While the split sounds are fantastic.
So, keep trying, BKP has something out there that will fit your needs and blow you away!