Check out the Advantage Hard Hat. I have had mine for about a year without issue. it seals well and sits flat like you are describing you would want. Folds up nicely or you can just remove it in about 2 minutes if necessary. It comes with either a vinyl top or a canvas top (very nice) and is in your price range. My bed has been dry since I bought mine. i have yet to see any water in my bed. I have a Bedrug so maybe there has been a little but I have checked and never seen any. I think you would be very pleased with it. Check it out.
Yeah AFM! Didn't like it so I tuned it out. Can't tell that I'm getting any worse mileage since tuning. Not sure you can convince me that a 6,000 lb vehicle running on 4 cylinders is going to save fuel! By the way, I like my truck a LOT better now that it shifts like it should and I'm getting more of the engine's potential.
Let us know how those perform for you. I'm in the market to replace the SR-A crap myself. I really like the look of those. Makes the truck look much better without going up much in size.
Don't think this has been mentioned but I could have missed it. I ultimately ended up with the Advantage Hard Hat Premier cover for my truck. I really like the way it looks on my truck and it gives a good bit of security as well with the hard shell under the canvas. If you haven't checked these covers out, I suggest you do so, especially if you are interested in the Extang Trifecta cover. I will try and post a picture soon as I don't have one yet with the cover on the truck.
I wouldn't want this truck either with all that is wrong with it. If they didn't want to just replace with a new vehicle, I'd let my attorney start talking to them.