1993 Ford F-150 F-150 ran great 'till we replaced pan gasket

We just replaced the oil pan gasket on my ''93 Ford F150 XLT, 5.0 L. What a major pain ! In order to remove the pan, we took off the intake manifold, dropped the exhaust system, and jacked up the engine 4 inches to remove the oilpan & install the new gasket, (as per Ford service manual). When we put the engine back together we installed all new gaskets, (Yes, they were the correct ones). Now there is a "whoshing" sound that lasts for about 4-5 secs, when we turn the engine off, that I never noticed before. The engine runs smooth, and has about 20 lbs of vacum when running. As soon as you turn the engine off, there is a loud "whoshing" sound and the vacum drops to 0 lbs ! The sound seems to come from the intake manifold. We double checked & retorqued all the bolts. We checked all the vacum hoses, and all are attached & have no breaks or leaks. IS THIS "whosh" NORMAL OR HAVE WE MISSED SOMETHING? Also, nothing appears damaged on the back of the engine from jacking it up.
When the engine is shut off, and the "whoshing" noise starts, there is suction, INTO THE ENGINE, on the breather pipe that comes out of the value cover and goes to the air filter! It appears that the normal air-flow of the engine reverses when it is shut off, because this pipe is normally sucking fumes OUT of the value cover.

Since everything seemed to be working fine, we test drove the truck. It ran smooth, and had good power & pick-up. After 8-10 mins of driving, the "check engine" light came on. We pulled over, and checked everything, and found nothing wrong. When I started the truck up again the light went out. After another 8-10 minutes the light came on again. We once again pulled over and checked eveything. The light seems to come on ONLY after 8-10 mins of DRIVING. We left the truck idle in "park" for 20 mins and the light never came on. There are 105,672 miles on the truck. Is this a pre-programed, "bring your truck back to the dealer because you have X amount of miles" dummy light? Or is there a vacuum issue going on here?

One other thing, the idle did drop down a couple of times when I came to a stop sign. When I gave it gas, it hesitated a little, but never died. Also, when we put it in "park", after driving it for about 30 minutes, the idle went down, then up to normal, and down again and up again, several times. It smoothed itself out after about 5 (down & up) cycles. It sounded like it was going to die, but it never did. Like I said before it runs great with plenty of power & pick-up. We turned the idle up a little but the up-down cycles still happen when it is it "PARK", idleing after being driven for a period of time (engine hot).

One last item. The OLD intake manifold gasket was soaked with oil and the inside of the manfold was full of oil & the bolts weren't very tight. No the rings aren't bad, because the spark plugs are clean and dry and it dosen't use any oil. I'm sure the intake manifold had to be leaking before, and we just didn't know it. Maybe because everything is sealed now, that the vacuum system is acting up?

This really has us confused because the truck had NO issues or problems prior. This engine has never been overheated or abused, or pulled a trailer or anything.

Buy the way, the pan gasket doesn't leak a drop, (The reason we started this whole mess in the first place).

Would one of those error code readers that you can plug into your system help me out? Which one would you recommed? Thanks