[Bored chemist]

It's a simple matter of kinetic energy transfer , which I already broke down . 

No.
It does not matter how many times you say that, it will not be true.
You need to do the momentum calculation.
A ship can lose energy to the rest of the universe by radiating heat.
It can't lose momentum without something to push.

[Professor Mega-Mind (OP)]

Momentum = Mass × Velocity .
Two ships are inside a giant box , they launch from opposite sides , tethered to giant reels .  Before they collide , the reel-drags activate , bringing the ships to a halt .  Their momentum drops to zero , the box never had any .  Where the bleep did the momentum go !? Come on , I know you got this !
P.M.

[Kryptid]

Momentum = Mass × Velocity .
Two ships are inside a giant box , they launch from opposite sides , tethered to giant reels .  Before they collide , the reel-drags activate , bringing the ships to a halt .  Their momentum drops to zero , the box never had any .  Where the bleep did the momentum go !? Come on , I know you got this !
P.M.

Assuming that your two ships were identical to each other, then the entire box-ship system had zero momentum throughout your entire scenario. Each individual ship has momentum when considered in isolation, but the fact that they are traveling in opposite directions from each other means that they cancel each other's momentum contribution out from the viewpoint of the entire system. Momentum is a vector quantity: it has both magnitude and direction. The momentum of this system was zero from the beginning to the end.

[Professor Mega-Mind (OP)]

So NOW the overall system is the point ! 
Haha !

[Kryptid]

So NOW the overall system is the point ! 
Haha !

It always was.

[Bored chemist]

Where the bleep did the momentum go !?

Wrong question.
Where did it come from?
The ship moved forward because its propellers  pushed the water backwards.
That water pushed on the big box.
And the momentum of the water + box + ship system never changed.

But, if there was just 1ship in the box and you were watching carefully from the outside, you would see the box move one way when the ship moved the other way.
Then, when the ship stopped- because it dropped anchor, or the rope went taught or even it just shut off the engines + coasted to a halt; the momentum would be transferred back to the box+ship+water system.
And the box, as viewed from the outside would stop moving.

The box would have moved slightly (in the opposite direction to the ship).
The centre of gravity of the whole system would have stayed still throughout the process.

[Professor Mega-Mind (OP)]

"It can't lose momentum without something to push ." Your words .
My words : The space-ship's momentum was transferred into additional momentum of the elec-trons , atoms , and molecules , of the reel-drag mechanism .  Heat stores a LOT of energy , that is why a little fuel goes such a long way . 
"Hey Rocky , watch me pull some momentum out of my hat !" .
P.M.

[Bored chemist]

My words : The space-ship's momentum was transferred into additional momentum of the elec-trons , atoms , and molecules , of the reel-drag mechanism .  Heat stores a LOT of energy , that is why a little fuel goes such a long way . 

You really need to get to grips with the idea that energy doesn't have a direction but momentum does.

[Professor Mega-Mind (OP)]

That one direction becomes many directions when the object's momentum is transferred to a multitude of electrons .  Heat is normally omni-directional .
P.M.

[Bored chemist]

That one direction becomes many directions when the object's momentum is transferred to a multitude of electrons . 

How?
In every single collision of every atom or electron momentum is conserved- essentially if the impact came in from the left, there's no way to stop it being unsymmetrical.

[Professor Mega-Mind (OP)]

It is not so simple on the atomic level .  The shock of impact causes vibrations and shock waves to propagate back and forth throughout the material .  The components of the material may also shift around , rearranging their directional orientations in the process .  Lastly , electrons in an electron shell act more like a trapped wave , than a circling particle .  They do not preserve directionality the way a free electron does .  This is why when you apply  a disc brake , the resulting heat is omni-directional .
P.M.   

[Bored chemist]

They do not preserve directionality the way a free electron does . 

Yes they do.
Because, at every single stage, momentum is conserved.
You still insist on muddling energy (which is dissipated) and momentum (which isn't- leading to you going over the handlebars if your bike stops suddenly).

All you did then was patronisingly try to say that you are right because you are right.

That's not going to work on a  science web page.
You need to admit that you are incapable of doing the maths.

[Professor Mega-Mind (OP)]

Your Humble-Pie awaits at "What is the best..." .
Also , they're just different descriptors .  Kinetic energy is simpler to phrase , as in KE=M×V .
Calculators , get used to them !
P.M.

[Bored chemist]

Also , they're just different descriptors

No. They are fundamentally different things- as I already explained. Momentum has a direction; energy does not.

Your Humble-Pie awaits at "What is the best..." .

I didn't see any.
I just saw you showing that you can't do high school maths.

Calculators , get used to them !

Unlike you, I am well enough used to them to recognise that they don't really do mathematics.
They do arithmetic.
So, once again,
please show us your calculations of the momentum transfers in the scenario you put forward.

Also, don't waste time posting anything else.

[Professor Mega-Mind (OP)]

Time for YOU to vacate , since you keep begging me to .  Your arguments have NOT disproven MY process , only misrepresented certain parts of it . Your H.S. math has been based on these mis-representations , while mine is based upon obvious , rock-solid , "Arithmetic" .  It's kind of hard to deny that 2 + 2 = 4 , now isn't it ?  To the readers out there , I say "Dive right in and do it yourselves , just use the straght-forward process AND math I've laid out , and you should get observable results .  Ignore the negatives and their smokescreens , and you should be good to go !
P.M.
P.S.- I work Sundays !

[Bored chemist]

It's kind of hard to deny that 2 + 2 = 4 , now isn't it ? 

Nobody sought to do that.
However if someone asks you "what do you get if you multiply 3 by 4?" and you reply
"2+2=4 ", you have sill given the wrong answer.

It's not that you get the arithmetic wrong. It is that you are doing the wrong arithmetic.

[Professor Mega-Mind (OP)]

Well , be that as it may , 99MJ still outweighs 1MJ any day of the week .  I stand by that fundamental logic , especially since no one has debunked my actual design .  I've been researching it for enough years !  I'm a good sport though , and am willing to entertain others presumptions and beliefs , as long as they don't  bite at me too hard !
P.M.
Note - I consider the "vacate" talk a form of running away .

[Kryptid]

Kinetic energy is simpler to phrase , as in KE=M×V .

That is not the correct equation for calculating kinetic energy. The correct equation is KE = (1/2)mv². The equations for momentum and kinetic energy are not synonymous.

[Professor Mega-Mind (OP)]

I said the full equation earlier , that's just the idea , which by the way , I stated for the easy understanding of the uninformed !
P.

[Kryptid]

I stated for the easy understanding of the uninformed !

Which means you told them the wrong thing.