John lets answer a few of your questions here.
1) The rock trap has nothing to do with over/under shelling of corn. It will be full of ears in the first 5 seconds you go down a row. The rock trap is for when you are harvesting small grain crops. When you are running small grains the rock trap will not fill up like this.
2) The top adjustable screen/chaffer. It has two handles because the front is set with one handle. This controls what falls on the bottom screen/sieve. The other handle is for the rear foot of the chaffer. This controls how much of the grain/trash drops straight down into the tailing auger.
3) You adjust the sieve by opening the door under the back of the chaffer(#21 in the picture) you pull the two spring loaded latch handles toward the center of the combine (#20) The door will hing down so you can reach in and adjust the bottom sieve.
4) In 200 bushel corn with a six row head on a JD 6620 you are really maxing out the combine's thrashing capacity. Usually you maybe right around 2 MPH maybe a little faster in low moisture corn and a little under in high moisture corn.
Now to set your combine for maximum capacity in corn. Forget what the setting say are the minimum and maximum. They are just a starting point.
Have the combine full. Do a power shut down. 1) stop the forward motion with the hydro. 2) Pull the kill knob out and kill the engine while the separator is still engaged. Do this quickly. You want the combine separator to stop as fast as you can get it too. Then disengage the separator. Restart the engine an let it cool down
then shut it off. You will not plug the machine up doing this. This will allow you to see where and what the corn is doing in the machine.
1) Check to see if you have whole corn cobs on the straw walkers (there is door right behind the grain bin on the top of the tail housing) If they are split then open up the concave until you are getting 80-90% whole cobs. The indicator on the concave adjusting linkage may not have been zeroed out so I rarely use it for anything but a starting point. You need whole cobs not split or broken cobs.
2) Now with whole cobs you need to slow the cylinder down until you start to see corn left on the cob. Then just speed the cylinder back up a little until the cobs are clean and whole. I usually just run a little ways down the rows. stop for just a minute then back up to where you can see the cobs that drop off the chaffer in front of the header. This allows you to get it close without getting in and out of the combine so much.
Now we need to set the chaffer.
1) I usually start with the front about 3/8-1/2 inch open. The back section about a 1/4 inch wider.
2) Set the bottom sieve at about 5/16-3/8 to start.
Run the combine until you have the separator full. Do another power shut down. (I am only telling how to do this as you are very new to the machine. after you run it awhile you will not have to do this)
By doing the power shut down you will be able to look on the top of the chaffer and sieve an see where the corn/cobs/trash is. So if there is still a lot of corn to the back of the chaffer then you need to open it up just a little so it falls through more toward the front. If the sieve is full of corn then it needs opened up a little so you are not returning as much. If the sieve is full of too much trash/cobs then close the top chaffer a little.
After you have set it then run the machine. You can check the tailings by opening the small door in the cab under your left heal. If it is running clear full then you will need to adjust on the chaffer or sieve some more. If it is mostly corn then open the sieve some more. If it is cobs and trash then close the chaffer some. After you have done it a few time it will become easy for you.
I have not mentioned the fan speed. In corn you usually run the fan wide open or as fast as it will go. You would have to be in real low test weight corn to blow any out. You do need a lot of air flow to separate 200 bushel corn. In wheat/oats/soybeans you may have to reduce the fan speed but usually only in oats will you have to lower it very much.
The fines you see on the back axle are normal. If you get the machine set correctly, like I have talked about, you will minimize them but even 1% loss in 200 bushel corn is two bushel per acre.
When you get the machine separating like you want and the loses are where you are happy. Then you can set the Harvest track monitor. Have the selector set to monitor both the chaffer and walkers, combined. Have the seed size knob set to the largest size. Operate the combine at the speed where you have everything set for the losses you want. Then turn the top knob to adjust the needle to be centered in the green on the readout. So when you start to lose more than you have it set for it will show it.
I know this is kind of long. If you have questions email me and we can exchange phone numbers so I can walk you through some of this.
Your cob tops in the bin is more than likely the concave set too close. The cylinder at 320 is kind of on the slow side. Remember the settings can change from one variety to another but you usually will only have to adjust the concave for cob size and the cylinder speed for how hard the corn shells.