There are built in holes that have rubber plugs in them currently, that would be used for draining out the interior. Most people who do a lot of water fording pull those plugs out when they get to the water fording and then drop them back in later when it's dry. Others simply throw them away and never look back. I am not sure how much water would get in if you are driving in the rain/snow for any period of time.
Locally, I see TONS of folks just strip the carpet out, and then prep and rhinoline the floorpan, the walls, roll bars etc. This increases the noise in the cab significantly in my experience, especially at freeway speeds, but this would be the best way to solve your water retention for hosing out, but noise may be an issue for you. Usually this is done on wranglers ime, and they pull the doors and tops at the first excuse they have (if they even put them on here), so it doesn't matter as much to them.
As far as sound deadening, the NOICO products on amazon come highly recommended from my coworker who does lots of car audio stuff, I haven't done any price comparisons vs. dynamat.
the paint and primer you choose is going to depend entirely on the layers you are going to follow it with.
If you are going to put sound deadening and vinyl floor over it. I would just use their standard line of automotive rustproofing paints/primers, I have not had a problem with them but be aware that ANY paintjobs quality is highly dependent on the surface prep and quality of the substrate (no amount of rust converting paint is going to save a rusting body, just delay the inevitable).
I couldn't open the morris 4x4 link, tried through google too and still couldnt. never actually opens/404/fails, just keeps spinning.
I have used "vinyl floor kits" on several vehicles with varying results. usually they fit a little loose, but nothing unusable. IIRC the kit maker offered options for backing/padding including waterproof versions, but they do add cost.
In one I just installed the vinyl directly on top of the existing carpet because I didn't want to pay for any kind of backing/padding at all, and I didn't want to loose that sound deadening effect, it worked very well in that application, but you could tell there was something thick under it as opposed to the OEM carpet fit.
Only you can decide if it is a good idea to drill MORE holes in your jeep, and the placement would be in any low lying areas that would be likely to pool water.
Now that you have me thinking about this, I would probably strip the interior(probably not the dash though, just the trim/covering on it), re-run the wiring to get it off the floor/hidden/away from where my feet/the water will be(this is the hardest/most time consuming part IMO, and I think necessary for doing this correctly), then prep the surface for linex/rhinolining. I would try to work it out with the painter so that I do the prep myself to save some cost.
After that is complete and I put the seats and time back in and I would drive it around and see if I (and SWMBO too) can deal with the noise on long drives. If not, I would approach sound deadening from the exterior, either rubberized undercoating, or stick on mats, or both if I can or if it is necessary.
Then I could pull the plugs anytime I like, hose it out and let it dry, then pop my plugs back in. I would not drill any new holes unless necessary get the drainage, and I would make rubber plugs to fit the opening (castable silicones/rubbers are easy to work with and you can layer aluminum foil over the opening to make a mold for yourself, let it set and peel the foil off).
