Scarecrow71

There known issues with TweakScale, so I wonder if thats it.  My suggestion is to remove both mods and see if things work.  If that does work, install one and check and repeat.
If that doesn't work, and potentially.before you uninstall anything, try verifying your files through Steam to make sure the files aren't corrupt.

There are two ways to get the rover to stop, but both require you to have control of it AND you need a Kerbal or probe on it.  You can either:
Hold B until it stops, or Click on the parking brake (to the left of the altimeter). Alternatively, you could use retractable wheels and keep them retracted until you get a Kerbal seated.

Even with the scripting module, of you don't have certain things unlocked you can't use all the features.  In this case, you need at a minimum Flight Control.  I have found that anything less than Advanced Flight Control makes MJ nearly useless.
You will have to manually stage and throttle until then.

The 2 non-part mods I'd recommend that aren't listed are MechJeb2 and Kerbal Engineer Redux.

The only way is to uninstall the mod.  Personally, I recommend having multiple installs of KSP.  Myself, I've got a no-mod install, a light mod install, and one that I really need to clean up with all the parts packs.

Time has almost no real bearing on the game other than for transfer windows and time to travel somewhere.  Not that I've found, anyhow.  I know some people want to conserve as much time as possible, but I think that's just a personal thing.