Wow - had a look. There’s a lot here. Had my level 10 finger yoga workout with [ctrl]+[alt]+[shift]+[m]!
I specificly looked at the duct work in the theater building. I assume you want to apply smooth to the ductwork and that is why you are having to deal with non-manifold edges.
There are considerable manifold problems and I don’t have a single solution for you at this moment.
since the geometry of the ducting is symetrical delete half of it and create a mirrored duplicate (linked)- this will half your problem at least.
(1) select and delete half the object [x], vertices (edit mode)
(2) [alt]+[d] (obejct mode)
(3) mirror it [ctrl]+m,  or select X (if I remember the placement correctly)
You can also use the Mirror modifier.
In the sections that matter you could try converting the mesh to quad-faces - there are lot of tri-faces used when welding sections together. Because the model is so large I had to scale the model down alot to see the normals - this helped identifying problems.
Did you use a lot of booleans to shape?
If you could highlight your need to get rid of non-manifold edges there might be some better/targeted help to offer.