1. I would run them in parallel. You would then end up with a max output of approximately 40 amps at 40 volts. That 40 volt output allows you to use a relatively small diameter cable. If you wire in series, that resulting 160 volts probably exceeds the max voltage rating of some (maybe most??) charge controllers.
I've found that my flat mounted panels produce a maximum of about 85% during the summer months and about 60% during the winter months. This is mostly in the desert SW so sun conditions are good most of the time. Assuming similar mounting and numbers, you could then expect about 1200 watts during the summer and 850 watts in the winter (for reference below).
2. This is related to your battery bank so a chicken or egg sort of thing. I've had great success with MorningStar (and their tech support and the problem wasn't even theirs) so I would recommend a MorningStar MPPT. I have no experience with any other brand but there are some good ones (and some not so great ones). It is important to understand that these (Morningstar TS-MPPT) controllers will output the rated amps regardless of what the battery bank voltage is or how much power the panels are providing. For example; the TS-MPPT-45 will output a maximum of 45 amps. If the battery bank is 12 VDC, that would be 45 amps VDC. If the battery bank is 24 VDC, it will output 45 amps at 24 VDC. Wow, they say - that is effectively doubling the capacity of controller. Right! Since these controllers are not free, this is one good reason for a higher voltage battery bank (no need to have multiple charge controllers). Another good reason is the reduced size of the cables required (to the inverter, for example). Of course, this comes with the cost of having DC-to-DC step down converter(s). I'm running 24 VDC and have as many 24 VDC components as possible - inverter, water pump, some lights, etc. but you still end up needing a step down converter as many things just aren't available in 24VDC. If you choose a 24VDC battery bank, the TS-MPPT-45 will meet your needs (1200 watts / 27 volts (charging voltage) = ~45 amps). If you go with a 12VDC battery bank, even the TS-MPPT-60 won't be able to take full advantage of all the power from the panels, you'll need a unit (or two) than can handle approx. 90 amps at a charging voltage of 13.6 amps. Btw; you can "overload" these charge controllers, the excess power is simply "clipped" (not used).
3. I'm not sure there is a "best" - each has its own pros and cons. I chose a 24 VDC bank given the same issues as you are currently wrestling. A year later I am still happy with that choice.
4. That is entirely based on your needs and use. Some folks want to have enough battery capacity to run 2-3 days without any sun at all, others have different requirements. All of this depends on what equipment you are running. Here is an example of the energy audit of my last motorhome - maybe gives you some ideas.
Dutch Star Energy Audit - JdFinley.com
I wouldn't worry too much about the charge rate vs. bank capacity rule of thumb. In my opinion, it is a nice ROT but may not be possible given our reality. Additionally, solar doesn't always charge exactly as you expect - think early morning sun or cloudy day, etc.
Linear Mode
