@Formula350 sorry about this, but when I said it cleared it up, I thought it did. But when I went in to work on the code, it seems the engines used method b already. I think I need to explain what the setup actually is. It is 4 engines that use method b or something similar, and they work fine. The problem lies in the cosmetic VTOL engine that creates the afterburner affect. I will just tag you on the upload and see what you can do.

@Formula350 I’ll most likely be able to do the burners myself, but I am on iOS so might do the burners, then reupload as an unlisted craft and tag you so you can help with the wings if you still want to do that. Thanks for the help!

lawl Ran into the character limit again, but thankfully it was just this that got cut off:

If that doesn't solve it, feel free to Upload your plane, but set to "Unlisted". After it uploads, place a Comment with @Formula350 in it, to summon me there, and I can download it to see if I can figure something out to help.

@AdmiralCrab Re: Wing Scaling
I don't know if this will work out, but it'd be something to try... (this is assuming use on PC, as that's the only platform I have SP on)
1) After you've got them scaled how you want, select it and open up Overdrive, select everything in the location field and CTRL+C to copy it to clipboard. (then close the window, that's all we needed)
2) Now on that selected wing, Right-Click-and-Drag with the mouse, to make a Copy of it. Preferably somewhere that it isn't connected to anything, although it's fine if it is.
3) The "Copy" of it will automatically (or should be) selected, so once again open up Overdrive.
4) Highlight the contents of the Copied wing's location field, and CTRL+V to Paste the coordinates of the original wing.
.
So now we've made it so there are two wings in the exact same location.
.
5) Open up the "Wing Properties" menu, and change the Root and Tip thickness to slightly less-than whatever it is. This is just to 'fix' the issue of the one visually showing up partially through the other (in texture/gaming, this is called "Z-Fighting", as both try to be rendered).
6) If while Copying the wing, you allowed it to attach somewhere, open up the Attachment Editor and remove all of them, then click Auto-Reconnect.
7) Now press Tab on your keyboard, to mirror that part over to the other side.
[Note: I personally prefer to do the mirroring before the connecting, but it takes a couple more steps to make it easy on yourself, and not zoom inside the other part to select it. Either way I prefer it only because I often run into situations where WAY MORE parts than I wanted, also get mirrored, resulting in more work in the end.]
.
Now both sides should have 2 wings, which hopefully will translate into 2x the lift. I don't know if the "violent shake" you experienced is due to lack of lift, or the Center-of-Lift changing drastically when scaling the wings down, or something else. My hope is that it's just lack of lift, and this improves that, but if it doesn't make any difference it could be due to the CoL being in the wrong spot.
.
OR it's just that you're going way too fast for the wing physics. Even full-scale wings can experience this, and while you may not have had the issue before, changing their scale could very well have changed how their Physics are calculated. (Basically, I could see it as if you scaled them down 50%, that they may experience this speed-wobble at a 50% lower speed than before.)

@Formula350 1. Thanks for the help with the burners, that really cleared them up! 2. I mean the actual XML scale.

When you say "scaled down", do you mean the actual XML entry which by default is 1,1,1?
OR
Are you referring to using the Edit button in the Wing menu and then dragging around the Arrows?

Afterburners...
A couple ways I've seen it done:
A) through adding more Engines and then having them turn on when a new Action Group (AG) is toggled, to provide the extra thrust, both visually AND physically.
I'd configure that like this...
The Primary (non "Afterburner") engines would get whatever settings and AG to operate them. If you have 4 Engines (as it sounds like), each one gets turned on by its own AG and are controlled via Throttle
The Afterburner engines would then have their AG all set to the same, say 5, because this is only needing to toggle them when you want "Afterburners" enabled. The trick then is in their input code where you include the AG of the Primary engine it is providing the Afterburner for (so replace X with that number):

ActivateX=1 AND Throttle=1 ? 1 : 0

This is a dual purpose "IF" statement that needs to have two things satisfied to work: The AG has to be enabled (that's the =1), and also the Throttle has to be 100% (also =1). The ? then is what to do if both are true, and in this case it's "make this Engine's input value 1" (which is it's throttle level, aka 100%). The Colon is what to set if they both are NOT true, which is 0 (throttle = 0%).
.
B) The other way, which I kind of think is better as it uses less parts (but may not offer the same function you're after), is to NOT use additional "Afterburner" engines, and let the Primary engine do its own Afterburner! Basically here we use the same code from Method A. First we tweak it so that your engine normally works as it would, but in Afterburner mode it increases its own power. Second, and more importantly, we put it in a totally different spot; max instead of input!
This method, itself, has multiple ways to tackle it, but the simplest way is to add this to each Primary engine's max field:

ActivateX=1 AND Activate5=1 AND Throttle=1 ? 1 : 0.5

<CONTINUED IN NEXT POST... I hate these forum's character count limits!>

<CONTINUED FROM ABOVE>
Now it's "If these are both True" it lets the Max Throttle be 100%, but if they are not, it's Max is only 50%. It's only the Engine's throttle though, your red-bar while playing will still show as it always has. This may seem confusing, but keep reading...
Then you go over into the Engine XML category and change powerMultiplier to also be 2, as well as set the exhaustScale to something like 3,3,3 (ideal to make the scale be all the same number). Combined, this is what gives them "Afterburners", because now the engine's internal throttle is only 50%, giving it the same power it normally would have at 100%. HOWEVER, when you toggle AG5, it has twice the power, and its exhaust gets much larger to match! :)
NOTE: Your "Throttle" while playing, you'll still set to 100%, as everything here is happening behind the scenes.
.
After you set all 4 engines this way (Method B) you will be able to toggle each one On/Off with AG1-4, and then any that are turned on, when you press AG5 they will enter Afterburner mode, just as you desired.

@LarryTad since you seem interested too.

@KfcGaming You would think that would solve the problem, but they already are wing-2 types. The shaking only happens when they are scaled down for cosmetic reasons

If they shake use overload mod and change the wing type to Wing-2