Covered this a couple of times before, but here goes again......
In Lorin's case the suspension was lowered by removing spacers, but we didn't clean out the props - (having never had to lower suspension before it never occurred to him or us).
Lowering caused the props to be compressed but with old grease in there this can lead to hydraulicing issues putting extra pressure on the pinion seals and T/Case output seals leading to the leaks which is the most likely cause of the problems.
The key point to learn from this is if you lower your suspension, take the props off and clean them out before refitting with the new suspension setup and re-greasing.
Actually when loading up for a trip it would be worth getting the props off and cleaning and lightly regreasing the sliding joint because as the suspension settles you may have the same problem, particularly if you have under rated springs.
Back to the breathers, the standard breathers are designed with a one way valve in the cap so as the axle heats up the air expands and is expelled, but when the air cools down it isn't sucked back in so it leads to negative pressure in the axles. We have had axles on vehicles that have been sitting for a few weeks where there is still quite a loud sucking noise when you pull off the breather pipes.
True, there is some negative pressure in the air box, but nothing near to what you get normally in the axles so it isn't worth worrying about.
If you do a short pipe run from the front axle you can end up with some diff oil blowing up into the air box - Toyota recognised this problem so on post Aug '92 80s they started fitting a small plenum chamber on the chassis above the axle to catch that oil (which had been coming out off the breathers and causing blockages of the factory breathers). In some cases we will either extend the breather from the plenum chamber or we have a longer run up from the axle both of which reduces the issue of oil in the air box.
One final thing with plumbing into the air box, try to avoid putting the inlet directly into the path of the air flow where the air enters the air box - at that point the air flow is quite high and can lead to some venturi effect that may also increase the incidence of oil in the air box.
FYI, the main reason I went down the route of plumbing into the airbox is that it is a much neater solution, you don't have bundles of rubber pipes all over the place and don't have to mess around getting them up in to the snorkel head where they may be subjected to the 'ram effect' leading to excessive positive pressure in the axles and gearboxes
The only times we have problems with it now are with trucks with diff problems where the oil is getting cooked and we get vapour up in the air box.