1. a properly designed quality lift kit will raise the COG a bit but will not cause any more changes in the handeling, the ones that mess up the handeling are the real 'redneck' lift kits which are simply blocks between the springs and axles or body lift blocks Usually a proper lift kit only raises the COG about 1/2 the height of the lift (lift the truck 4" the COG only goes up 2"). You will sometimes see them labeled more like "supension lift systems" to show that they were a propery designed system rather than just some simple lift blocks.
There are quite a few 4x4 forums which give a lot of good tips for waterproofing.
2. Besides the snorkels you want to extend the vent lines for the axels and transmission/transfer case to prevent water from entering them but you should still change the fluids after fording deep water because some will still enter through the axel and drive shaft seals. So if this is your "bug out vehilce" you want carry enough spare fluids with you.
3. Keep the electrical systems dry. Relocate any electrical components you can as high as you can. Anything low apply plenty of tune-up/dielectric grease to seal the connections. I saw one site where they had a plasitc bag to cover the distributer.
4. if your fording real deep water you can get in a situation where the engine fan catches enough water to flex the blades and hit the radiator. You can swap to electric fans and wire an off switch in the cab to shut off the fan for a short time to get through the water.
5. the other problem you will run into is the carpets and insulation under them will get saturated with water and rot and mold and eventually rust out the floor if you leave them in there for a few years. I've seen the 4x4 guys with no carpet or ones that use truck bed liner in the inside of their vehicle.