We run mixed mode where I work mostly because in the even that something horrible happens to AD, we might still want into the SQL servers.  We have a group...

I agree... without more information there isn't much anybody can tell you.  
As a thought, which CTE is slow?

I'd test that first.  Select from each CTE 1...

I have a theory on this:
In GIT, do you have your BIN folder included?  if Visual Studio detects no changes, then when you click on "BUILD" it sees no...

Do keep us posted though... I am watching your progress on the Emsisoft forum as well as I am curious how this goes.

I am hoping for the best....