I am not completely sure I know what your asking.
Well, all I can say is that holding a piece to a time signature that it doesn't fit is a bad thing, in my experiance. My advise is that if you know it is in a different time signature, change it. I played a piece this last year that changed every two to five bars for most of the piece, and if anything it made it easier.
The main idea is that you are notating the piece. The goal is to be free of errors, and not writing it the way it is "supposed" to be is like using bad grammar or spelling words wrong in a book.
So, count the beats and make the revisions you know are there. frequent tying accross measures is usually a sign of a bad signature, IMO. (those off beats might also be indicators.)
hope this helped.
PS: from what i listened to (not all of it) sounds good.
PPS: messy score...