PJ my old rig was a high top with effectively a fixed bed in the back. I don't think it is what you would call "elevated". Personally, I wouldn't elevate the bed above the height to be able to see out the rear window. I always found the view out the back window minimal but very handy. I never 4x4 in that rig but went through plenty of trees; never a problem. Only place we got caught was we passed on some of the low tunnels of the Needles in South Dakota.
Also worth considering is if it is possible to lower any portion of the floor? I'm pretty sure this had been done in my rig and why; I at 6'2" could stand all the way up.
Honestly, if you're going to tear out the interior and swap the roof why not just sell the whole rig and start a new?