There was an obvious key clue in your post for anyone that really knows how PCM's work - it IS possible that you are losing a little bit of power (maybe 3% or so at most, but enough to notice at 40 mph when the engine isn't making any power to begin with) by driving the vehicle conservatively (normally), and that is simply the normal effects of adaptive strategy at work - unless you are using cheap gas, or have a clogged fuel filter, that is all that is going on, and that happens with any computer-controlled vehicle.
That is precisely why the truck ran great at first, but then, just exactly as you said, as you drove it more and more, it doesn't feel quite as strong - and it's noticeable in that scenario at 40 mph.

Adaptive strategy optimizes the powertrain operations for best fuel economy based on the manner in which the vehicle is operated most frequently - and even the most aggressive driver still doesn't spend 2%-5% of their time at WOT (wide-open throttle) - which is why as you drive it more after installing your mods, you seem to feel you have lost power. See, what happens when you flash the PCM with any tuning device is that it *also* clears out all previous adaptive strategy adjustments - same thing happens when you simply disconnect the battery for long enough, by the way - so the vehicle feels more peppy than "normal" when you first flash the PCM (even when going back to the stock factory tune). Then as you drive it, the more you drive it at less than heavy throttle, the more potential to see a small loss of power, up to about 3% or so across the board - it's simply adaptive strategy. Disconnect the battery for 10 minutes and you'll get that power right back - but then as you drive it "normally," you'll lose that 3% or so again. Perfectly normal, and it happens to everyone.

Now, can this be improved upon with our *custom* tuning? Yes, but only because we are getting larger power gains, not because it will negate the effects of adaptive strategy - you are always going to have that.

Another way adaptive strategy works on these newer trucks - when we were doing the tuning R&D for the 5.4 3V F-150, we found that once we tuned the vehicle and dyno'd it, and then took the vehicle out and drove it for a couple hundred *hard* miles, we gained another 8-10 Hp on the dyno.

It's not your modifications that have cost you power after you accumulated some miles after installing your modifications - it's simply adaptive strategy at work. The bottom line is, unless something is happening like using cheap gas and/or a clogged fuel filter (from using sub-par fuels), you are simply experiencing the normal effects of adaptive strategy as you drive it more.

Remember, you have a very heavy truck there, and only a couple of mild bolt-on parts - and that is not going to make a "big" difference in such a heavy vehicle when lugging along at 40 mph, especially trying to go up a grade - ion that scenario, th engine is turning maybe 1200 rpm, the TQ is locked up, and that is because you are not calling for any real power - so as you go up a grade, yes, you *do*( have to give it some significant throttle to get the TQ to unlock, the transmission to downshift and get some torque multiplication going & allowing the engine to make some real power.

I do have one tip for you - in the 1714, [edit - The SuperChip product in question - dmp]*go back in and alter the 2-3 shift point manually - bump it up by exactly 2 notches - and I think you'll find that will help your driveability in that kind of scenario. Remember, the engine has to be able to turn some rpms & have some throttle opening to make any real power.