97 Mercy, you are correct, the vacuum pump "dumps" all the air sucked out of the vacuum system right into the air cleaner.

That explains the fluid in your air cleaner, that is the only way any fluid is going to get in there besides it sucking in water (rain, carwash) or the EGR (which makes more of a soot black paste crap)

How on earth would the vacuum system vent the ATF into the crankcase guys? It should burn instead of being pushed into the crankcase by the positive crankcase ventilation system, shouldn't it?

Which vacuum line are you talking about? If you pull the line right off the modulator (passenger side of most trannys) and it has fluid in it then you know it's the modulator.