Even though you know that the deck is specified as 4 volt preout, don't use the markings on the amps to aid in setting gain. The voltage is invariably more at the higher freqs and less with the lower freqs. And it sounds like your input wiring and crossover selection is good.
I would leave all settings on the deck at flat and leave the enhancers off while setting gain. You are setting gain at the maximum clean playing level of the deck, where enhancers would not be used anyway. When it's all said and done and later as you play your system, you could emply the enhancers as needed at low volumes and it will not cause problems with the gain setting. Just set them back to flat before maxing out the volume.
Follow the instructions you noted about the bass remote control. The sub bass will always be attenuated from the maximum position, which will not cause problems with the gain setting.
You could set either amp's gain first. You want to listen to only the output of the amp whose gain you are working with, leaving the other amp disconnected from receiving input. I doubt that hearing protection would be an issue here, but if your sub is so loud it starts to hurt, use common disposable ear plugs to quiet the volume. The components will probably not require ear plugs while you work with them.
Start by choosing the highest clean sound level you can find with the deck output alone. Since the speakers are attached via the amps, you will have the amps' gain settings all the way to minimum while you test for the deck output. Use a variety of CD music sources that you're familiar with when doing this. You will already know which of your pro-recorded CDs seem louder and more dynamic than some of the others, so use them.
After establishing the maximum deck output, make a note of that level and never turn your deck past that again. Using your CDs, adjust gain on the mids amp until you reach a level of volume that begins to sound disrupted, indicating a clipped signal. Turn back the gain just a hair and listen again for a clear and precise sound. Leave this setting alone and test with a few of the other CDs you have chosen to test with. Once established, you now have the deck and mids amp levels adjusted. Adjust the crossover on that amp to get a full sound in the lower midbass region, as well.
Remove the input from the mids amp and start adjusting the sub amp. Follow the above procedure, also adjusting the crossover so that you can feel the drum kick but keeping the vocals at a very low level. And note that sub-bass freqs often are heard better from a distance, so feel free to walk about while listening for that disrupted sound.
After those two gain adjustments are done, it's just a matter of listening and tweaking. One thing you will do right away is listen to the system complete and make sure the sub tones are in phase with the mids. If there seems to be a slight beat of difference between them, you should switch the + and - outputs on the sub amp and listen to tell if that is a better choice. Leave the wiring where the music sounds loudest and most dynamic, which would indicate matched phase.
You cannot increase the gain on either amp, but you can decrease gain at any time if it seems to clean up the sound. Crossovers can be tweaked at any time. And any time you make a change to the system, this gain-setting procedure should be followed again.
Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.