As for the pipe actors, i believe they dont show up because of that doom builder 2 breakdown you did (you organized actors into sub groups to make mapping and placing actors easier).
Heres a pic of the actor in question:
actor number 31016 - pipe 2

The other pipes are also affected i believe. This is only one of them.
EDIT:
Im sorry Jigsaw that your map is lost. Btw, does anyone have the notepad file with credits done yet?