Hey Dan, just to confirm what you are experiencing with your TRD's, I have the very same problem with speed bumps, particularly the kind of those metal yellow half balls nailed on the pavement, no matter how slow and how carefull I pass over the speed bumps and my mudflaps scrape. I have the Tokico Luminas at the softest setting (sometimes I wonder if 1 is the softest or the hardest setting haha) with the TRD springs and just as you say, this suspension combo seems too low and too harsh a ride. To make matters worst, I also have the front and rear TRD sway bars.
I just went over my second back surgery and the doctors said I won't be able to ride my bicycles for at least a year, so I am also assuming I will have to go back to my OEM springs which fortunately I have kept over the years, and I will have to research about shocks too, so don't forget to share your experience with us so we can take a wise educated decision with the new suspension combo. Someone I can remember has the Koni shocks is either Randy (Redtwo) or Kevin (Sprinterkb) and I'm sure they would be more than happy to share their experience with you about those fine shocks. I would love to get my hands on one of those Koni sets to try'em on my Two.