The widescreen fix breaks the hive ship section of the game.

It is best to back the files up and paste the unmodded versions before the Hive railshooter. Then you can install the patch once more afterwards.

Tried that and it didn't work

Dang... Have you also tried playing with the game's resolution/graphics settings after you put back the unmodded files? I cannot recall if I had to or not. I had to make it run back at the original resolution.
Otherwise, I do not know :(

There is still a last resort "way" (if you care about the prizes from the mini-game) and that is using the CheatEngine to slow down the gameplay and give yourself better reactions to aim lower due to broken aiming. That is what I tried first before I reverted the files.
I know that is NOT a solution and I know that SUCKS but it is... something.

FYI for those who are having an issue where Sly or the NPCs start moving weird, or stutter step on screen (or moving at an angle despite only pushing forward)

If you have NVIDIA, go to your Control Panel and force Antialiasing to FXAA, set VSync to On, and set max FPS to 60. That fixed it for me.

The Widescreen worked perfectly as well.