Hey modifing the one you have is a really easy and cheap way to go, it appears to be a good rack just stick with what you have and make it work for you,
Ive built three different rack designs for my RTT and they all had the same idea.... low as possible. I would keep it and chop the top rail use the lower section and RTT till the cows come home!
By the way that a really nice looking rig you have.
Here is what my origanal set up looked like. the RTT was as close to the topper as possible made travel easier and getting to the zipper for the cover, as well as deploying it easier.