Yes, tranny, gas tank and both diffs have filters, crankcase stays in airbox which will be sealed with dielectric grease around rim and rad fan vent will either be looped or ran into air box via drain hole at the bottom of airbox then siliconed around. Snorkels will be painted black and the end caps are for when I pressure wash it, I dont want water getting in there.
Looking at your filters on my phone, I counted 3 venting systems at first. I see 4 now... well thought out.
If your open for a thought of mine, I personally wouldn't bring the radiator fan vent up thru the air box bottom drain and silicone it. I would come up higher in front or side of box (into the primary/dirty side of course) and use a 90° ell to take it inside. Maybe try to find the right sized bulkhead fitting and actually be able to tighten it up with the fitting's nut and silicone it at same time? That will leave the drain bulb accessible to pull off in case your air box lid fails to seal 100%, even when greased up if you will be fording water continuously. It would be nice to drain water out by pulling the bulb off rather than it sealed up and have to soak water out with rags etc. If you are mainly a mudder and not a river forder, then it probably wouldn't be a big yank to do you initial way then.