***"Disconnecting the motor isolates it to the mower itself, with that done i can safely say that it is not the starter, alternator, or the magneto."***
So, does the above statement mean that the 20 amp fuse is still blowing, even with the engine electrically separated from the chassis wiring harness?

Yes it is still blowing. I have replaced it with a 30 and it takes a few turns of the key but it still blows. I have taken the entire wiring harness apart thought i found a spot but was wrong. I have noticed that when i do turn the key that the green ground wire and the red with white stripe wire kind of "twitch". Not sure what that means. By twitch I mean they move they will move to one spot until I release the key then they will go back to the spot were they started from.

***"it takes a few turns of the key but it still blows."***
So, you are trying to say that it only blows the fuse "if you are cranking the engine"?
Have you tested to see if the fuse actually blows simply by turning the key switch to the run position......and leaving it there.....without trying to crank the engine?
It is important to know this because if this only occurs while you turn the key to the start (crank) position it really narrows down the possibilities.

It only blows in the crank position. I can turn it to the first position and it does nothing but once it goes to the next position it blows.
I found a video on YouTube and there was a safety loop on the alternator where the diodes blow out, i have checked them and they are fine.

That pretty much narrows down the circuit-
You might jumper in a 12V test light in place of the fuse-

On the starter solenoid is a small wire that receives 12V from the key switch to activate the solenoid.
Between the key switch & solenoid will be the PTO/attachment switch and the clutch/brake switch.

Disconnect the plug from the individual switches to determine where the circuit is intact and where it is shorted to ground.
There's also a possibility the key switch is kaput.