Caerfinon

if it's black, you haven't got the IVA configs and textures loaded. 
If you installed it manually, in the ZIP download there is an Extras folder that has the IVA information. Copy the contents of the Extras into your GameData.
If you used CKAN, then you need to install the separate IVA mod. 

Those boxes can be toggled on/off with the F4 key on PCs. Not sure what the binding is for MAC/Linux. 

Material kits are indeed part of Modular Kolonization System (MKS). To get them you can do one of the following; (the first is the easiest for your immediate purpose)
Launch a vessel with a Kontainer full of them and dock with the station. There are a number of "Kontainer" parts that can be set to material kits that you can load in the VAB.  Disassemble parts at the space station which will produce material kits, but you need a storage part to collect them into. Use MKS Manufacturing parts to turn metal, polymers, chemicals and machinery into material kits.  Use MKS WOLF background resource harvesting per biome to collect resources and turn them into material kits that can be transported and delivered to the station. Worth reading: 
MKS Wiki MKS Guide WOLF - Industry without the part count WOLF Walkthrough

Right click the tanks during flight mode, and lock them. Can be done in stock. 

Too Many Orbits can clear them out 
 

Did you recently uninstall a mod that had it's "own" kerbal traits?
If so, then there are likely "applicant" kerbals in the roster of your persistent.sfs that have one of these removed traits. The Astronaunt Complex, and the assign kerbals functions in the SPH/VAB are broken until these applicants with now invalid traits are removed from the file.   

It's not a one to one thing. Air intakes provide a resource to the craft and each engine requires a minimum amount of that resource to function. A single Wheesley might run on one small cone but two will have more demand for air than 2 small intakes can provide.    
If you use Kerbal Engineer Redux mod you can see the values required during design time. If you don't the stock value of intakes and engine requirements can be found here: Air intake and Jet engine

delete the 0 byte file. @thumbs create themselves during load. (There is no @thumbs directory in the mod ZIP from CKAN). Then start your game again and see what happens.  If it fails post your ksp.log and your player.log

delete the 0 byte file. @thumbs create themselves during load. (There is no @thumbs directory in the mod ZIP from CKAN). Then start your game again and see what happens.  If it fails post your ksp.log and your player.log

delete the 0 byte file. @thumbs create themselves during load. (There is no @thumbs directory in the mod ZIP from CKAN). Then start your game again and see what happens.  If it fails post your ksp.log and your player.log

delete the 0 byte file. @thumbs create themselves during load. (There is no @thumbs directory in the mod ZIP from CKAN). Then start your game again and see what happens.  If it fails post your ksp.log and your player.log

delete the 0 byte file. @thumbs create themselves during load. (There is no @thumbs directory in the mod ZIP from CKAN). Then start your game again and see what happens.  If it fails post your ksp.log and your player.log

Just the numbers...
Kerbin 2 Mun 3 Minmus 2 Moho 2 Eve 3 Gilly 1 Duna 4 Ike 1 Dres 2                ( just kidding, Dres "doesn't exist" ) Jool 0 Laythe 3 Val 3 Tylo 3 Bop 1 Pol 1 Eloo 3  

An engineer can activate EVA Construction mode by pressing the "I" key or by clicking on the hammer and wrench icon on the toolbar.
Then it acts like the VAB/SPH and the engineer can grab parts from storage within range and attach them as needed. 

An engineer can activate EVA Construction mode by pressing the "I" key or by clicking on the hammer and wrench icon on the toolbar.
Then it acts like the VAB/SPH and the engineer can grab parts from storage within range and attach them as needed. 

See -> https://answers.microsoft.com/en-us/windows/forum/windows_10-files-winpc/how-to-remove-a-default-file-association-app-from/3e498ed3-016d-4acd-847f-09c2470b711c

Then you are going to have to research each mod and its dependencies, and the dependencies of all the dependencies as well. Then you will need to get all of the proper versions of the resulting list of mods and correctly install them in your GameData folder. 

Parts not showing up correctly is typically due to the mod being installed in incorrect folders and the part config then not having the right path to the models and textures that it needs. This is not every case, but it is the better part of them. 

There's this one
// Add in-vessel transfer support to all parts that can hold science, unless // explicitly disabled by the part. This is the same ability that the stock // Experiment Storage Unit has; it doesn't really make sense for it to be // limited to just the that part. // Author: Wyzard @PART[*]:HAS[@MODULE[ModuleScienceContainer],!MODULE[KerbalEVA]] { @MODULE[ModuleScienceContainer] { // Allow "Container: Collect All" and "Container: Transfer // Data" by default. &canTransferInVessel = True // Allow targeting by "Container: Transfer Data" on other // parts by default. &canBeTransferredToInVessel = True } } from:
 

In the astronaut complex you can alter some of the suit colouring by clicking on the coat hanger icon in the kerbal's picture. A window will pop up alowing you to alter the suit types and change the colours on the future suits.
If you want to change the colours in a more extensive way, you need a mode like Texture Replacer  and either downloading a suit package or create your own.
You can find out more detailed information in this post
 

CKAN information is available in this thread. It is installed as a stand alone program on your device and then detects the KSP installations you have.
Updates to CKAN progress as the mod authors make them. Some are very current, others are not.
CKAN will give you an indication if one of your installed mods has an upgrade. CKAN will also resolve dependencies for any mod you choose to install and install the additional mods as well.
 

You could use Waypoint Manger It has a setting to show all, only active, or no waypoints at all. The latter setting turns off the stock waypoints as well.
 

Look under your account settings/signature

Look under your account settings/signature

Yes.  You need to keep your default EVE configs though (in your case AVP). 
Just remove the EVE folder from GameData and replace it with the EVE Redux  version