a little background 1st, truck was running great until Friday. we got 2-3 inches of rain in an hour while I was on the road and I submarined the truck. my bow wave broke about eye level on my windshield. truck started chugging about 1/2 an hour later with lots of white smoke. changed fuel filter, cleaned 22 years of sh** out of fuel filter head, blew out fuel lines, filled it with diesel kleen and she runs pretty good except... now there is a woofing sound out of the air intake and the bottom of the air filter had a puddle of oil. While she's running, the tranny dipstick smokes and when I shut her down smoke comes out of the air intake? WTF?
also when I accelerate she chugs, sorry don't know what else to call it

 

sounds like a open intake valve .... i fear the worst for ya as for the tranny you most certainly got water in everything rear end, tranny, engine, fuel tanks anything with empty space lol .. id say change everything oil wise and hope its just a sticky valve but im leaning towards something bent water dose not compress and 21.5/1 compression will bend something good luck im sure others will chime in on this

 

CRAP! I sorta thought that was what it might be, I was hoping someone was going to tell me I had a small dog stuck in the crankcase and not to worry about it

 

checked my oil and tranny fluid, don't think there's any water in them. neither one of them has that chocolate milk look. do you think it's safe to drive?

 

The smoke coming out of the intake is normal -- I'm guessing you have an old engine; you get a lot of blowby. This will come out of the CDR at the back of the intake; you can see it flowing forward in the air stream if you idle the engine with the air cleaner off.
When you shut the engine off, it will rise, as it's not being pulled forward.
I've worked on four of these engines, and all of them did this. I thought it was bad at first, but now I see it's normal(or, well, as normal as worn rings etc. is).

I'd just drive it for a while; you're probably still having fuel/IP problems. You aren't supposed to pour cold water on your IP, according to the manual, so something might have broken inside.
Still, if it runs, you're in pretty good shape.

Also, I've found that a lot of noises and issues can be caused by failed/failing injectors - One starting to leak sounds like a bit of knocking; one too high pressure/stuck sounds like missing/rumbling.
Timing also has a major affect on power and noise. Failing IPs can cause all sorts of weirdness too.

Not sure about the tranny issues; did it smoke there before?