So the file size "mis-match" is just a matter of your OS using a different definition of "megabyte". To be more precise, then, the file is 45,944,230 bytes. For a definition of 'megabyte' as 1,000,000 bytes, that's the 45.9MB I was seeing, and at a definition of 1,024,000 bytes per megabyte, it's 44.867 (with, presumably, some rounding error somewhere making that last digit not quite match).
As for the supposedly-missing files: those files, in fact, should not be there.
Delete your GraphicsLib mod folder, then re-extract a clean copy. If you still have issues with these supposedly-missing files, it's not GraphicsLib that's at fault, it's some other mod that's incorrectly referencing out-of-date file locations.
(Now, if you're running Starsector 0.96 with mods from 0.95 that haven't been properly updated, then maybe the merging you've done is the only way to get them to run. But if you're doing that, well, be aware that there may very well be other lurking gotchas from running out of date mods, and that you should test turning them off before attributing errors to mods that actually are up to date.)