Why are you hesitant on the brakes? They're great, as far as I'm concerned. Far more aerodynamic than on the 4 series, with no appreciable drawback. The rear brake doesn't get as dirty as in the traditional mounting location, and the front brake provides a better aero profile for the bike. Also, you're behind the 8-ball in terms of weight, because the 4-series frame is a good bit heavier than the higher level bikes. I believe that the 5, 6 & 7 series share the same fork (I asked my fork to run the numbers and they weren't able to find any difference in model numbers between the three).
If you're concerned about the weight of the saddle cap, I'm pretty sure that the difference in frame weight more than makes up for that difference, and the nature of the suspension it provides really smooths out the ride.
All things being equal, the added $400 is more than worth it, going with the lighter, more aero bike. I think the 5 series is the unsung hero of Trek's current lineup. Sure, it's a little heavier than a comparable 7-series (maybe 200g, at most), but it is just as stiff, just as strong, and leaves you with a nice canvas to upgrade.
Trek Crockett, Madone, Superfly, SpeedConcept & Cobia