Newbie questions

Well Im with you on this question on how much movement is ok between van body and camper body, I myself have concluded that there may be some but you really shouldn't be able to see or move it around and I figure this because the van is rubber isolated to the frame and the frame is super long, there is going to be flex or twisting. Now with that said and like in the case of my Shasta, both van and camper bodies are mounted via rubber mounts......... So I figure the van and camper should be tight and flex free as much as possible at least that what I'm going for on my Shasta rebuild. As far as the overhead bunk, you should not have any movement but remember and from my own experience all the parts need to be there like the outside trim channels etc in order to maximize strength. Might want to post some pics for us and maybe we could get a better idea of where your at.
I also reccomend. Checking out my 84 Shasta motorhome rebuild, may give you a good insight on how motorhomes of that vintage were put together (poorly)
One last thing and I really hate to say this but it kinda sounds like you have more structure damage than you think or repaired, water is a funny thing comes in at the front marker light and rots the kitchen floor out. And most I've looked at that seemed to be leak free turned out to be really bad.
We're ( I'm) here for ya, we will get you through this :)