I don't really see anything bad about that set up. As I said, even my pedestrian setup is beyond magnitudes better than the Raptor system was. The issue with using the factory Ford headunit is it's going to retain the factory EQ settings if you don't use a processor to unfuck them and level it out.
I'd say my only piece of advice is once it's all installed, take the extra couple of hours after installation and tune it and configure it properly. This is an amateur speaking here but it worked great for me and all my music sounds great. Find your best quality music that is composed the best and turn the bass off completely. Tune the EQ and high pass filters so the speakers sound good, you can hear all the instruments clearly, and aren't distorting at high volume levels. You'll want a little bit of lows (>125Hz IMO) in the speaker but obviously mids and highs. Once that's dialed in, turn the sub/bass back on, and set the bass remote to 3/4 volume then adjust the gain on the amp to what you feel is borderline too much bass. That way, depending on the song you're listening to, you can turn the bass remote down or up if the song isn't composed as good or has too much bass, etc.
I have my knob set where when it's in the middle position, it's just the right amount of bass regardless of what song. If it's an old school Lynyrd Skynyrd song with no bass, I'll turn the remote up. If it's Lamb of God, and I want to hear the crisp bass kicks but still want bass, I'll turn it down.