All of the customers I have install perforated tailing and clean grain cross auger pans and a perforated floor in the feeder house floor. Round bar concaves work very well, and some of them put a perforated section in the unloading auger. I prefer not to use the perforated in any of the augers because rocks get stuck in the holes and will crack beans. Close the bin cross auger cover as far as you can or you will have trouble unloading. Rotor as slow as possible and concave as open as possible and as much air as you can with out blowing out beans.
You will either have to dig out the auger if the beans are a little tough, or break the transition auger in the unloading auger and still have to dig it out. Yes the slides need to be nearly all of the way closed. How are you cutting the beans and what type of pickup head are you using?
I will second that on closing the cross auger slides all the way. We flexed a few pintos with our TX this year and even in good dry beans they will plug and it really sucks dragging vac tubes up the ladder then sucking it empty. Beats the heck out of shoveling though.