Geonovast

If OP isn't opposed to a few more mods, a little surgery with KIS/KAS could also have the same effect without having extra docked joints.

None of your links work, they don't appear to be public.
 
But if you CoM and CoT are lined up, which I'm guessing they are since you appear to be proving a picture with them displayed, then my first guess would be that your "Control from here" point is upside down, and you're launching with prograde on for SAS.
Either that or there's an insane amount of drag at the top pulling the top of the ship down.
See the link in my signature on how to directly imbed your pictures.

You can see in this picture that the decoupler to the right of the orange vein is significantly further away from the vein than the one on the left, so that's probably causing issues.
You also have the fins on the twinboar clipped into the boosters.  This won't be a problem... until you decouple them.  Once they're decoupled, they become different ships, and being clipped inside will cause weird forces to act on your rocket.
Same issue with the fins clipped into the launch stabilizers.  You can hit the launch stabilizers once you detach on launch.
And you want to strut to the parent.  So the outer boosters should be strutted to the one they're coupled to, and the inners should be strutted to the rocket's core.
 

Hello, and welcome to the forums!
If it makes you feel any better, you're definitely not the first to run into this.  There's actually another thread just a few down the list with the same issue. Hopefully something in here will help!
 

To get to orbit: Go up and sideways.
To come back down: Go sideways the other way, but just a little bit.
To go to a different planet: Go sideways a lot more.
Z goes.
X stops going.
B stops going faster.
Space bar turns things on.  Make sure you turn on the right things.
Pointy end up.
Hot end down.
 

Check this out.  I actually use it to prevent anyone from jumping in a pod, forcing me to pick crew every time.
 

Flipping high up generally means that you have too much drag up front, or that your CoT is too far off your CoM.  Once you start running out of air, your flaps can't compensate for it anymore.

Also, as @1101 said, don't timewarp a spaceplane ascent.  Physics timewarp is far from perfect.
You may also want to get some gimble capable engines.

(Assuming you're not on console)
Install KAC, and set an alarm for the transfer.  KAC will stop the warp at a pre-determined time before the burn (IIRC default is 1 minute, but you set the time)
 

Thats the offset tool.
Upper left of the screen in the VAB/SPH, to the right of the parts list are your tools.  Place, Offset, Rotate, and Reroot

Yeah, that's what you would do.  Normally I would say back up the current persistent.sfs, as as it's corrupted anyway, it probably wouldn't make much difference.

Did you update all your mods with the game update?
It's probably Scatterer.  Remove it and see if the problem is still there.  If the problem goes away post your issue over in Scatterer's thread.  If it's still there, keep removing your mods one by one until the problem disappears, then post your issue in whichever mod's thread was last removed.  But I'm pretty sure your graphical problem is caused by your graphical mod.
 
Also, log file, log file, log file.  You will definitely need your log files when you post your issue in the mod's thread.
 

Just lets you set a second key to do the exact same thing.
I haven't used it much, but I have my Map View secondary key set to my 'Forward' mouse button.  Pressing the 'Forward' mouse button or 'M' will toggle map view.
Did the same for the 'Back' mouse button with screenshots.  Pressing the 'Back' mouse button or 'F1' will do a screenshot.
 
It's also handy to set up mapping on a joystick, and you can switch back and forth from the joystick and keyboard without remapping every time.
 
Also thought I'd mention that I'd set my 'Forward' mouse button to cycle symmetry count int the SPH/VAB.  Makes editing a bit smoother since I don't have to take my fingers off of WASD when placing parts.

The persistent.sfs is probably corrupted.  There should be a backup folder inside the save folder.  Rename your current persistent.sfs file something else, then pull the most recent backup out of it's folder into the save's folder, and rename it to persistent.sfs and try again.
Might set you back a little bit, but better than losing the whole thing.

There's a small circle down to the left of the Kerbal's portraits.  If you click on that, it will give you a cutaway view, and show you the inside of every part that can house a Kerbal.
You can also click on their portrait, and tell them to go EVA.  If they're in a part that has door, they'll go outside and the camera will instantly focus on them.

Greetings!  Welcome to the forum.
I use TAC, and it seems to work alright with me.  Unfocused vessels use supplies, and Kerbals most certainly die when they run out.  I don't know what TAC was like when you last tried, but I can say that now, both of your issues are options in the difficulty settings under TAC.

 
If you have those set correctly and it's still not working, check and make sure you have the right version for your version of KSP.  If that's all good, it would be best to head over to the TAC thread and look for support there.  (There's instructions in the first post on what they want in order to help you)

I had the same happen to me a few days ago.  Rolled back the driver and everything was cool.
Wasn't just KSP, I had other programs that quick working.

So THAT'S what that does!  I've always wondered.  I don't use advanced tweakables, yet the UI was always there and seemed to do nothing.  Every time I saw the truss I just figured it was a mod.

I have the GoG version on Linux, so don't really know if it's applicable to a Mac.  But I simply made a copy of the GameData folder.  Renamed it GameData.stock.  I put all my mods into the original GameData folder.

If I want to play stock, I simply change the modded GameData folder to GameData.modded, and change GameData.stock to GameData.  Now I'm playing stock.  And vice versa.  This lets you access your saves under both "versions" as well, since they're not kept in GameData.