Bagleman..You are simply AWESOME taking this project on good luck!!
From what I understand, that "tape" you mentioned getting is used/sandwiched between the aluminum frames and side-walls the frames screw into. If you were to take any of the aluminum "edges" off your rig, you would find that stuff behind them...its sticky and will mean your removal of aluminum edge rails will not occur without completely bending and damaging them beyond re-use! ...don't ask me why I know this to be true :-(
My guess would be when you remove your current bunk end frame, you will find that tape there...it almost looks like plumbers putty. From my experience, when you place it back in it will help hold and seal things up as you screw the new frame into place. My recommendation would be some high quality RV sealant (Dicor made for walls?) to seal the joint between your frame's and sidewalls when your done and you shouldn't have any future water leaks. Like others have said, I can swear I read a story of someone doing this themselves but the only Goole searches I could find were people having dealers do it. My thoughts are as long as you take your time, there should be no reason why with help you won't end up better off than you were previously!
If your open to it and inclined to do so, I am sure there are plenty of folks on here that would LOVE to see pictures and stories of your effort!! hint hint ;-)
Ed & Chris
Josh & Jaclyn
2012 Suburban LTZ
2013 Rockwood Roo 233S