Upon looking closer, it appears that it is bolted up to through the clutch assembly to the shaft...is this correct? If so all I may need is the correct bolt, does anyone know the size? I am nearly an hour away from the nearest JD dealer and it would be easier to hit my local hardware store if this is at all possible.

I've seen a couple of these do this and it was a broken bolt. Look up into the crank threads for the remains. It may just turn out w/ the edge of a screwdriver if luck is with you. For hardware needed it is just a standard square key for the drive pulley, a double heavy cupped washer at the base and the bolt. If you decide that is all you need, the parts counter guy would likely tell you the size and grade. I suppose you could use a double flat washer and a lock washer and be OK. Obviously, the right hardware and the right torque will hopefully keep this from reoccurring. The bad news: If you are saying that the wire is pulled out of the PTO clutch, then you will need a new clutch anyways. When the clutch is reinstalled, it positions itself in the keeper bracket to keep the out part of the clutch from spinning.

Thanks for the reply, it is a broken bolt....and its about 1/8 inside the shaft with nothing to try and get ahold of. The wire didnt pull out of the clutch, they broke where they plugged into the fitting coming from the deck switch. Problem is.....what can i do with the driveshaft. If I have to replace it, that likely means the end of this mower.
At least for me.

There are a variety of tools available to remove the broken bolt from the crankshaft.

You center punch and drill the bolt then use a reverse (LH twist) drill bit or EZ out to remove the broken piece. If the piece is stuck then repeated shots of PB Blaster might loosen it up.

It sounds easy and might be or might not be. If you break an EZ out they are hardened and a real PITA to remove.

DO NOT MESS UP THE CRANKSHAFT OR YOU'RE IN FOR A VERY EXPENSIVE REPAIR.

If you're not really good with tools then you might check with the dealer or local repair shop and have them do it for you.

There are a number of methods for removing a broken bolt.
The best method for non professional folks is to take it to a professional mechanic...and let him remove it.
This is a rather specialized skill sometimes. It all depends on your level of competence and tools.
So, if you want to try it yourself, follow JAL's advice above.
But know when to say "Uncle!.

Any theory as to why the bolt broke in the first place?

Is this failure common?

Once the PTO is installed and the bolt is torqued, there is not any additional stress on the bolt during use (other than maybe heat expansion)....

The couple that I did I don't believe were ever apart before. No signs of trauma. Neither reoccurred to my knowledge. I still service both. Fortunately, I was able to sneak the bolt out w/ a sharp tipped # 0 screwdriver or pick. Maybe a light tap w/ a punch could help. Both the screw and crank are hard, so it isn't likely that the threads fatigued and mushed together.

I use a Dremel engraver as my first choice when I encounter a broken bolt where the break is below the edge of the bolt hole.
I place the tip of the engraver near the outer edge of the bolt circumference and slightly tilt the tool so the engraver tip is hammering/vibrating in the direction to loosen the bolt (CCW for most bolts).
If the bolt thread stub is loose in the hole. the vibration of the tip makes the stub sort of "dance" in the hole and quickly backs it out so you can grab it with pliers.
I have actually used this trick to coax bolt stubs completely out of holes where there was not even enough room to use pliers. In those cases I learned that it is best to relocate the engraver tip from the broken face of the bolt over to the threads themselves after the stub emerges from the hole. Keep moving the point of contact so the engraver tip is always right near the edge of the hole for maximum effect.

Used an Isomay easypower bit I picked up at a True Value. I got the 1/4 in size and it worked like a charm. It only went about 1/8 or even less into the broken piece before it pulled it out. The broken piece was only about 1/2 in long.
Thanks for all the replies, I was a little concerned messing with the crank like that and told myself I was going to give it one try before taking it somewhere. The "pucker factor" was pretty high at first but it was only a matter of maybe 1 minute before it was done.

Extracting broken bolts from crankshafts either the pucker eases immediately or you stay puckered for quite a while.

Get the correct bolt and belleville washer and torque the bolt to spec.