The NA's do not have an AFM/MAF so you are never going to find it
The IAT sensor is normally connected to th OEM air box, but if they installed an aftermarket piece then it needs to go somewhere else. It sounds to me like you have a match as to what piece goes where.
I just have a pipe with a cone filter on the end of it on my NA and the IAT has just been laying around for a couple of years. I have not noticed any difference in performance. I would not, however, want an open hole letting in unfiltered air like it sounds like you have.