After a LOT of time spent looking for rack that was compatible with my Retrax and talking to reps from several companies, I finally ran across the Tracrac SR. It's a sliding rail system and the uprights are removable, so that's a bonus. It ain't cheap by any means but it works with what I have and it's going to do what I need.
What's really odd is that the CS rep at Tracrac told me she didn't think it would work with the Retrax. Then I talked to Retrax and they sent me to a photo on their website that shows the Tracrac installed with a Retrax bed cover on a F150. Nothing like knowing your own product, right?
Now, the SR system installs ising expandable plugs in the stake pockets. No problem with that, except the rails for the Retrax partially cover the stake mounts. Retrax would have happily sold me new rails cut out for the stake pockets for $315. Wrong.. My Dremel tool with several cutoff wheels did the job just fine, especially since it's going to be covered by the rails for the rack uprights, and 30 minutes later I have exposed stake pockets ready for rails.
It ain't very pretty, but it will be hidden.
I'll update this thread with photos as I install the rack, just in case someone else has the same set up that I do.