First off, this is NOT my first post. I used to be "DanLW", but since the whole password reset thing, the forum admins have ignored my multiple requests for a reset. Guess I should have kept my e-mail current. Mods, if you can help, please PM me. I can prove I am really "DanLW" if somebody would just listen.
I have an iNuke3000DSP hooked to my subs. (do a search for "Salerno Subwoofer")
I can't answer all your questions, but here's what I can answer.
Set your AVR to LFE+Main. Sometimes a sound mix will send stuff in the 20Hz range to your left and right mains. You want that sent to your subs for two reasons. First, your mains probably won't be able to reproduce that low of a frequency. Second, it takes the power drain off your AVR and lets it use that power for all the not low frequency effects. With regards to the crossover, let your AVR handle that. The only reason you would use the crossover in your iNuke is if you were running a subwoofer off one channel, and a midrange off the second. 80Hz is the generally recommended crossover point in your AVR, but if you feel comfortable with Room EQ Wizard, experiment with different crossover settings. With my Klipsch RF-7 IIs, 40Hz measures out as my ideal crossover point for smoothest bass response.
For the limiter, you may want to set one since your subs are rated for 400W continuous. But... I notice a different problem with those subs. They're only rated down to 40Hz. Is this for music or movies? You really want to get down to ideally 20Hz at least. (my subs are tuned to 11Hz) If you stick with these subs, you're going to need to set a high pass filter which is easily doable with the iNuke. If you send a strong 20Hz signal to them at high power, that could be bad juju.
Back to the limiter, you won't need it. The amp is rated to 1600W... AT TWO OHMS. Your speakers have an 8 ohm impedance, and at that impedance the iNuke will only provide about 400 watts per channel. So if you send it a prolonged 0dbfs signal you might damage the subs. But you may actually blow the fuse first. Go to the configuration tab in Remote Connect, and you will see that if you set the impedance to 8 ohms, it tells you 451.6W is where the limiter is set when it it set to 0dbfs (no limiting)
You mentioned a 20 amp circuit. You won't need one unless you add more amps. I have all my equipment running off one 15A outlet, and I was doing bass sweeps at high levels about a week ago. The fuse in my amp blew, but the circuit breaker in my home's circuit breaker panel did not. (I have since replaced the fuse, and the amp works fine)
Since you are running your amp in "Stereo" mode, just be sure any EQ changes you do to one channel you mirror on the other channel.
You are right not to use bridge mode. Bridge would basically make the amp operate as a mono amp, and would route all the power from both channels to one output.
Is I read through your post for some final thoughts...
For your mains, I have to disagree with Behringer... you would not set left and right speakers that play down to 55Hz as "Large". They can easily see signals down to 20Hz (and lower if you listen to some kinds of music) You need to set them as "small" (even thought they are physically large, if they don't play down to 20Hz, they are "small".) Your AVR will then route signals below the crossover point to your subwoofers.
But again, 40Hz (I see you listed 35Hz) is not low enough for movies. THX recommends 20Hz. A lot of bassaholics on this forum (myself included) recommend lower. But if you want to go that low on a budget, I'd recommend checking out the DIY section. If you already have woodworking tools (or need an excuse to buy woodworking tools), DIY is the way to go if you want big bass. If you don't have woodworking tools, perhaps check out HSU Research. You can get a pair of comparably priced subs that will play down to 22Hz, and lower if you want to spend a little more.
I hope this helps!