motorbreath,
1) Nothing wrong with the Rainiers. They are too new to the industry for my liking without much of a proven track record. We put a LOT of miles, normally, on our rigs, and I didn't want to find out how good or bad they were the hard way.
2) I have used Eternabond, and it's great, but I prefer something I can redo, easily. I have had great success with the Proguard stuff. Eternabond is almost permanent to some degree. VERY difficult to remove. I prefer to have the option to undo or redo if I want. I have nothing against Eternabond, I just don't use it much. I prefer the thick liquid method, as it fills every void, it's very thick, and I can see the seal. It is applied with a brush or roller (I used a brush), so no caulk gun needed. Some will argue with my opinions and methods, and that's ok, but I've used it for a good while, full timing, etc, and it holds up very well.
3) You are spot on with building your own. I was going to do this since I weld and fabricate a good bit. Just so happened I received a generous donation to the cause, and bought the MorRyde. I prefer not to weld directly to the spring hangers, only because it may create issues with a tank removal or the underbelly being removed later. Not always the case, but possible. LCI's similar fix does show a direct weld of a cross member. I prefer the bolt / clamp method. I can remove and reuse later if I want to. For what I paid, I probably will put them on the next rig.
4) Nothing wrong with your idea at all. The factory Chloroplast is tucked up above the I-beam and self tap screwed to the cross members. Some manf do this (tucked), some don't (just screwed to the I-beam). I like it tucked, although harder to remove, as it's looks a little neater and doesn't require any holes in the I-beam itself. I say go for it. You have the chance to do a better job, and better insulate. I also prefer to create access points for different things. Beings you will be installing an enclosed underbelly, now's a good chance to run a heat duct to your liking, and / or install 12v heat pads to the tanks and valves.
5) Never heard of moving all of it underneath, but have seen a lot of great vibration isolators made, all home made contraptions. Wood, foam, wood sandwich with pump mounted on top is just one of those I've seen. Also have seen rubber, springs, and other stuff. Anything to isolate the vibration. I'm guessing the vibration noise is the biggest aggravation. Pros and cons to installing pump in underbelly. Freezing being the biggest issue, maybe.