Ed (nice to meet you, by the way),
Is the 32-oz bottle an absolute requirement? I can think of a few options you can check out, but I don't know if they have room for a bottle like that unless you can tell me exactly how big the bottle is. and the molle might not be there either. I've heard awesome things on travel-related sites for the "Air Boss" from Red Oxx. It's designed by someone who does tons of traveling, with places for a laptop, clothes, and assorted pens, cables, and other stuff like that. it comes in several colors including a plain black, but ti's made specifically to avoid having stuff sticking out on the sides. the designer had seen WAY too many luggage locks and other stuff getting ripped off luggage by conveyor belts in airport-baggage areas and other situations, so there is no molle on the outside. it does have tons of pockets all over it and a very-well padded laptop slot in the middle, with clothes going into two more slots so they serve as a secondary layer of padding. the interior compartments also have mesh pockets and stuff to organize small things too. however, this bag was designed to look more like a soft-sided briefcase than a backpack, but I think there's a way to change the straps to wear it like a backpack. they are quite durable, and usually for a good price, but I don't know the exact price at this moment. I'll look into them more for you, to see any recent sales or new design options or such.
another option I thought you might consider is some sort of "gym bag" as either a duffel bag with straps you can wear as a backpack or there might be a backpack designed to use as a gym-bag. the ones I've seen (admittedly, not recently) usually have a mesh pocket somewhere big enough to fit a pair of sneakers in, so you don't have smelly or mud-covered shoes all your clothes and stuff inside the bag. all you might need to do is get some foam padding and add it inside for the laptop to sit, and I'll try to help you look for a good but cheap type that would protect your laptop.
there's also a few bags I've seen for new dads, hold tons of weirdly-shaped things without looking exceedingly adorable so guys don't feel as silly walking around with it. the interior space might be good for your laptop, but I don't know exactly how well it would be padded. Maybe you could get a separate padded sleeve or cover that fits your laptop from amazon or similar, then slide the laptop in its sleeve into the backpack? and there might be space for your water bottle too. I think the one I saw was all black, but there might be other clothes I don't know about. and I'm not sure if any of them have molle inside or out. They might, or might not. I'll check that out too in a couple of days.
if you're really picky, have you thought about searching locally for a seamstress that might be able to just make what you want? I would offer to sew it, but I don't have any experience at sewing the types of materials used in backpacks, duffels, etc so I wouldn't feel right about letting you put your laptop into something I might have messed up without knowing it.
I know these might not be what you're looking for, but I thought that you might run across something that would work for you.
let me know if this helps or if I didn't guess something right. tara