On D1's I'm pretty sure the front diff and transmission breathers are vented at the top of the firewall ... at least they were on my RRC. The rear diff runs up by the rear door IIRC. Getting them much higher isn't good for alot unless you plan on pretending to be a submarine
after deep crossings you will want to empty the water out of your swivels and make sure there's still enough grease in there. If there are signs of the swivel seals leaking or allowing water ingress (like a cups worth; they all leak a little bit even when new) you want to get them replaced.
As for the ECU, alot of folks seal it inside a tupperware container, cutting a hole out the side for the wires and using silicone to seal up the hole.
Get a good tube of dialectric grease and apply to every electrical harness plug you can lay eyes one (and even some you can't, like the ones that route under the carpets). Use it on your plug wires, and all the connectors on the engine, especially leading up to the coil packs.
with the moderate prep listed above you can be safe up to the grill / tops of the tires with no problems.
