I went and got the vaccum diagram for the 98-2000 2.5L from the FCO site and follow everything best I could. Well I found everything anyway! Everything looks good. I was able to carfully run my hand down most of the lines and could not feel any crack or abrasions. So am about as sure as I can be that I do not have any vaccum leaks. So what the hell is that sound I am hearing? I might actually try taking my laptop out with me and do some recordings of it.
As for the MAF sensor. I unplugged it and let her warm up. It ran horrible! Actually felt like I had a few wires crossed. I ran down the road about a mile and pulled over, turn the car off, pluged the MAF back in and everything seemed ok. After about a mile or so more, I slowly rolled the throttle to almost WOT and not a single stumble or surge. I was only able to hold it there for a short time, so I couldn't say where or not it would not surge. I only ran it for maybe 50 yards under these conditions. After reaching the middle of the left hand turn, I stabed the throttle and she locked up sweeter then... well you know!
I am starting to think that they might have shorted out the PCM at some point in the repair of the tranny this last time because of all this (confusing the PCM with the unpluging and repluging of the MAF w/o reseting). The P0743 also mentions a "short to PCM" in it's definition.

Then again, it would run worse than this wouldn't it?