Texasjohn, I really appreciate the input here. I've taken your suggestions and made some changes. (See file below) I agree, a few more posts and the 3rd holding pen is done, and that could make a big difference in the whole operation. I hadn't thought about our backs being open from holding pen #2. I think this also gives us enough circular paths to be able to double back around like you mentioned and close the entrance gate.
I also noted a "safe zone" where the cattle will not have access. This is where we could set up a table with meds and stuff like that and not have to worry about it getting turned over except by the ranch clutz (that's me). I added a gate at the top of the safe zone into the sorting pen. While the animal is squeezed up most of the gates at the top could be open allowing for easy access all around the Dube chute. That safe zone would also be a place for the grain as it is "interior" so any smells would lead the cattle in, not stop them at the entrance gate, but it's also easily accessible for those with opposable thumbs.
Incidentally I'm considering the gate into holding pen #1 as the entrance gate, it's in a corner which should help prevent animals from missing the gate.
I took out the raised platforms, we can always build them if we want. What about angled sides in the alley way? This is to keep the animals from trying to turn around in there. I've seen this on many systems. Is it worth it?
I got to see your tactics in action the last couple of weeks. The guy who's helping me on my farm while I get all of my equipment and learn how to run the place is also grazing some of his cattle on there. He's taken calves off the last two weeks to the stock yards. He does exactly what you mentioned, leads them into a pen by the barn and feeds them. Let them spend the night in there to get comfortable. Then when he needs to work them or load them they come in very easily. Actually, every time they even see me in the barn now, just getting my tractor out or something, they all come down to the corner where the gate is and just stand there patiently in line waiting for me to open the gate.

When we bring the feeders out to my farm we'll be mixing them with his seasoned cows to start, so hopefully this bevior will transfer nicely.
When I'm thinking about working the animals and potential problems, the bull is the one that comes to mind because of his SIZE!

But yes, the cows I'm sure can be a problem as well (hormones

). We have two matriarchs of the herd, the alpha & beta females if you will. They are awesome, I swear we could teach one of them card tricks if we tried real hard. Very smart, very docile, never challenge the fence, respect our space as well as want theirs. We were giving a tour to an investor and he wanted to know how the watering tanks worked, as we were explaining, as if on queue, Maggie walks up demonstrates pushing the ball out of the way with her snout and takes a big drink. She followed us all around the field, keeping her distance, but very helpful on the tour.
Another reason I talk about bulls a lot, is that we don't just have
a bull to deal with, we have more bulls than cows. The bulls flesh out so much better for beef. We do cow/calf stuff, but also buy lots of feeders (300 - 500 lbs) to finish off (>1200lbs). We have about 40 bulls right now all different sizes, several getting near 1,000 lbs. As things pick up we'll be adding bull feeders faster than cows. The feeders need less grass than a cow & calf, so with limited land we are going that rout right now.