DrLicor

Looks like you need this  
 
 

Here, try this one. Seems like opengl is causing it:
 

Did you downgrade to 1.2.2 before or after installing CKAN.
Make sure you firstly downgrade, after that instal CKAN. 
Also make sure that you have no remains left of the CKAN and KSP of 1.3

Hmm, that's indeed very strange, looking at your list, there's also no mod included that would take care of stage recovery, in case that would tricker it or something like that. 
Persistent rotation is only able to control the rotation of a craft, so that one isn't the problem, but you could try to turn it off to be sure, since that's quite easy to do ingame
Mechjeb often gives problems when the versions don't correspondence, you could do a double check if you have the right version. 
Same is actually for realism overhaul's dependencies.. 
The only mod else that comes last on my mind is ModularFlightIntegrator.. It's a depence of the RO pack I believe. Just a double check.
 
Also as last option that I could think of, does it happen with all the stages, hasn't it to do with a certain part(pack/mod). For example launch a SRB in the air and see if it also gives the same results. Maybe it's a corrupt part, which is quite unlikely, but just to make sure. 

Did you delete the Squad folder in the Gamedata folder? 
Also, I think the fastest way to get everything back is to reinstall the game via steam.. Just make sure that you manually clear all the files you've put in by yourself.

The drills go into the ground don't they?
Also, what are the advantages of these over normal landing struts? Landingstruts are much cheaper and most important; lighter. Which saves you a plenty amount of delta-v. 

The game will give you more valued contracts if your reputation gets higher. 
Also, if you download contract manager, you can disable the whole toerist thingy.

Torque is for all the 3 axis, as if in a resultant of the the forces that don't go trough the Center of Mass.
The Torque however is different for every craft, it depends on the weight of the craft and the thrust an engine provides, you don't need to look at the max torque, but at the max torque compared to your crafts mass. 

However, if your engines gimbal, you don't have to worry about flipping over because of the torque, as long as the CoM is in the range of the gimbals  
How can you see that? Well, there's an awesome mod, called RCS build aid, but you can also balance the other engines.
Most of the time I make sure the thrust goes between the dry center of mass and the wet center of mass. 
Also, with the mod installed and activated, you can gimbal your engines inside the VAB and SPH with the keys J, I, K and L and see how much torque they can produce/counter.
Hope this helped you.
~DrLicor 

You can make a tweakscale MM-config, just look how tweakscale does it to other configs. You can open all the configs with notepads etc. Everything that writes. 
Or you could just open the config of the part you want to scale, and search for the line scale = 1. Can also be scale = 1, 1, 1. (x-axis, y-axis and z-axis) Or tweakscale.
The scale goes in factors, so if you remove the 1 and add a 2, your part will be 2 times as big in all axis. 
 

Normally that only happens when you are in the atmosphere or you are accelerating in space. 
When you want to go back to the spacecenter, you need to land and stop or splashdown. When in space, you need to make sure you have no engines running. Somethings you spacecraft accelerates due turning, because the center of mass is moving. Yep kerbal physics so stopping your rotation can also help.
 
If none of the above is the problem, I think you should upload your savefile so we can reproduce it.