InfernoSD

If you have a save from before the kraken hit, you should return to that and try again. When you load in to the satellite, there's a few things you can try to calm the kraken:
Shut off SAS if it's on. (Circle) Shut off the moving parts. This may be difficult if they're already moving, but easy if you have them bound to an action group. Lock the moving parts. Once they're locked they become very hard to move. Deactivate and reactivate autostruts on parts affected. Autostruts create a lot of stability when set to heaviest part, but they sometimes need to be reset between stages and dockings. You may need to enable Advanced Tweakables in the settings to see this setting. Time warp. This usually resets parts to their intended positions. You can post images in the forum by uploading them to an image host and copying the direct URL here. 

I can't believe this bug still hasn't been fixed.
The game tracks whether or not you currently have the "More Info" window open on the part selector at the left side of the screen. It continues tracking this even for parts that don't have a "More Info" window and even while you're not even focused on the part selector. While this window is open, some of your camera controls switch to scrolling the window up and down. Or at least they sometimes do. The game is very finnicky about whether you can scroll that window or not.
Anyway, the solution is to return to the part selector, choose any part with a "More Info" window, and press Square to hide the window. Camera controls will instantly return.

It's a glitch specifically with auto time warp, and it only happens on first activation. Something about those first few frames of accelerating to a high time warp speed causes the glitch. Note that it's not the manuever itself changing, but the position and heading of your vessel, which can be proven by monitoring things like apoapsis and periapsis before and after engaging auto time warp. The manuever only changes because it was repositioned, although you may be able to fix the manuever by adjusting it again by any amount.
You'll find this problem goes away if you manually enter time warp instead. Go at least to 5x time warp. Then it doesn't matter if you manually warp forward or auto time warp ahead from there. You may still see a tiny jump in the orbit of your vessel, but it will be much less than with auto time warp.