Okay gentlemen here is my best "how to" for the KX500AF. I'll address the five biggest obstacles I encountered and some people who were very helpful.
We'll assume two things. 1. You have a KX450F as a donor bike. 2. You have a KX500 as a donor bike.
First, The swingarm bolt on the KX500 is smaller than the swingarm bolt on the KX450F. (15mm vs. 17mm) To allow for the larger diameter bolt you must drill out the case halves. I think it is necessary to split the cases to do this. Splitting the cases allows you to rest the flat side of the case halves on the deck, then mill out the hole assuring a square new hole and proper swingarm bolt alignment.
Second, This is the aluminum cut and weld part. A good man Dave at Absolute Engineering was good enough to help with this, it is hard to get someones attention with these small hobby projects, but Dave likes the smell of Premix. First you will need to cut out the motor mounts that are along the bottom tubes of the engine cradle. Cut them in a manner that they could be reused as shown by KXsinoz
http://www.kxriders.com/coppermine/displayimage.php?album=112&pos=13. Next, the wishbone is not in the right spot for the exhaust header to pass through. It must be raised to clear the exhaust. To remove the wishbone I cut mine right above the weld that holds the cast lug. The cast piece connects the downtube with the two engine cradle tubes. Again remove it in a manner that it could be reused
http://www.kxriders.com/coppermine/displayimage.php?album=112&pos=12. The amount of work to reuse the cast piece is intense. Or remove it entirely and fabricate a new one
http://www.kxriders.com/coppermine/displayimage.php?album=111&pos=14. With these cut out of the way you can now rest the engine in the cradle. I set the swingarm bolt in place and rotated the engine to accomodate all of the motor mounts then built the wishbone around the new engine position.
Third, Exhaust is also labor intensive. My first choice would have been a custom cone pipe, but I could not locate a fabricator that was anywhere close to me. I ended up using a CR500 lowboy pipe and silencer, as well as a few pieces of the stock KX pipe
http://www.kxriders.com/coppermine/displayimage.php?album=111&pos=1. I asked some questions at my local shop and here on this board about pipe dynamics, probably the most important factor was the length of the header tube before the expasion begins, then the length from there to the largest diameter of the expansion chamber. I tried to match those of a KX500 pro circuit pipe. As I was fabricating the pipe I could not say if it would have been easier to just cut up a KX pipe or my route. The Zip-Ty pipe also looks like it would be a good start. When the cutting was done I held the pipe as it was being welded to ensure good silencer alignment.
Fourth, Radiators at first were intimidating. My exhaust pipe was too close to the left side radiator, I needed to cut the bottom tank to clear it
http://www.kxriders.com/coppermine/displayimage.php?album=111&pos=6. I sent both rads to the good people at Mylers motorcycleradiators.com. They were glad to help and do some bench racing as well. I had the hose necks cut and reangled to allow the hoses to follow the same route as the KX500 (from pump to bottom R.S. radiator, up and over to L.S. radiator then down to the cylinder).
Fifth, Connecting the carb to the airbox was easy. I tried to use a KX450F boot, but with using a reed spacer, rad valve and PWK39, the boot just pushed back into the airbox too far. I ended up using a KX500 boot, air filter, air filter holder, and air filter cage. To mount the 500 boot to the 450 airbox, I made a simple adapter plate from flat stock 3/16" black ABS to cover the 450 airbox opening, then I cutout the opening for the 500 boot. A piece that Kawasaki calls an "Air Filter Holder" works as a great template for both cuts. Thanks to demographic for answering some dimension questions before I had the 500 boot.
I don't think this project would have been realistic if the cases were wider than the swingarm would allow. Machining the cases or the swingarm would have been a big ass can of worms. When I first realized this was not a problem, it was clear to me that this project was meant to be. As if the Kawasaki engineers wanted it to happen, the two sprockets align perfectly the kickstarter looks like it is supposed to and I can change the plug with ease.
Thanks again to everyone here for their help and I would be glad to send out my dummy motor parts if you can use them.