Ok so first things first.

Do any of the files that have be overridden been modified by any of your other mods?

Secondly, starting to come back to me now. Pretty sure almost all if not all of the header files were out of date? Check the file version compared to the dynamic filter ones, I think I had to merge them.

Don't worry about cannonical, that doesn't do anything at this stage. All it will do is ensure that your canonical links in the source are correct when the filters are applied.