First, you are far from a simple fan dude. You're one of the best posters we have on this site, and I value your input on many things. Now, to the nitty gritty.
Let me preface this by saying that I am not the best or most knowledgable guy on here to ask, but I'll try my best. Anytime you look at making a scheme, you need to consider what the opponent does. Like you said, there's a lot of rub stuff, a lot of slants, a lot of PA, and a lot of Clark. Then, you need to look at who they have to do it. Manning, Wayne, and Clark are the keys to the offense. While they do run some PA stuff, it is anciliary to what that trio does.
It is well known what Manning goes to the line with. He reads a defense, makes his protection call, attempts to force the coverage to show pre-snap, makes his check, and executes the play. Obviously, the key here is to create illusion. It's not about disguising something, it's about showing Manning A and giving him B. Further, it is about giving Manning a read that will cause an anticipated check, and then defending that check. The Colts understand this, so much of their passes are constructed around patterns that are effective against both man and zone.
Such is the slant. The slant is fundamentally about body positioning. When you have a reciever like Wayne, who is in that apex of a career that blends athleticism and veteran play. If you play zone, it's a complete ball underneath and a tackle. If you gamble and try to jump it, it opens the Sluggo and you are liable to get burnt for six. If you play man, Wayne positions his body to make the grab. With a corner draped over, he catches the ball for a short gain. If the corner risks stepping in for a pick, he could also get burnt for a sizeable gain after the catch. The key to defending the slant patterns is not letting the receiver get off the line, and if he does, take away the inside release. Bodden is one of the best press corners in the league. If I were drawing things up I would tell Bodden to ride Wayne to the sideline, or not let him get off. So, we have the first piece taken care of. Bodden, you take Wayne and bully him for 60 minutes. I would give him a loose bracket over the top from the free as well. You can't rub a defender if one of the recievers is stuck on the line.
I think where that intermediate flood works is with Clark. First, I would make it a long game for him. If he's going to get off of the line, it will be because he beat McGowan off of the line. If he catches the ball, SS Pat Chung is going to decapitate him. I doubt Clark's heart, and I would challenge it as a starting point. I would play mostly in a 33 nickel, McGowan playing as a 3rd safety assigned to Clark. Meriweather is assigned to roam back there and make plays on deep balls as the cover 2 free, Chung assigned to stick anything that crosses his vision. Make it simple for the rookie, let him play assasin from a cover 2 look. Thomas at sam, Mayo in the middle, Guyton as the will. I would blitz one of them except for in obvious situations. If not, their coverage is assigned to occupying the middle of the field, and pick up Addai on any release. Obviously, a blend. Meriweather is assigned to roam back there and make plays on deep balls as the cover 2 free, Chung assigned to stick anything that crosses his vision. Make it simple for the rookie, let him play assasin from a cover 2 look.
Well, my inbox is fairly daunting right now, so I gotta stop this before I geek too far, but I hope that it was fairly helpful. If I missed anything, or was ineffective in answering your question, please don't hesistate to ask.