I ended up running eternabond tape over all of the outer flanges of the slide. We had all of the inner flanges off (flat steel top and angle aluminum at the sides) and I sealed them with Geocel Pro Flex sealant. I also ran an extra bead of sealant on the inside edge of the top rail so that if water finds it's way on top of the slide room it won't soak through onto the headliner. I have confirmed this was successful.
Since we had the entire slide room out and replace all seals and rollers (along with subfloor and flooring) I find the slide lines up way better and seals contact fully when in and when out. I just have to let a little pressure off when it's out so the bottom isn't pressed harder than the top.
My remodel/renovation project still isn't done but it's close. We replace paneling in the bedroom along with all the carpet. I'm almost done redyeing the leather couch, captain chairs and dash (light grey instead of the off white factory). Pictures will be posted sometime when I'm all done!