Regarding similarity of controllers etc: If you build a multi motored plane, buy all the motors at the same time from the same source. The mfrs do change things in the motors from time to time. Buy all controllers the same way for the same reason. Buy Castle as you can put the same software version in all of them. Castle has a great tutorial on their site that gives many recommendations on seting up multis. You may not need a separate battery eliminator circuit. Castle controllers have ample BEC's up to 3S (12V battery) and you can combine the BEC's when you 'Y' the throttles together.
SBEC is a brand name as is UBEC. They are switching power supplies that convert the high voltage of the motor battery to 5 or 6V for your radio gear. koolflightsystems.com has a way to use 2 UBEC's for redundancy.

I built a twin and used most of Castle's recommendations. It is like an F-82 (twin Mustang) but is made of 1.5 Stevens Aero CAP 232 kits. The fuselages are about 24" apart and so I elected to have no interconnections. That's right, 2 batteries, 2 receivers, etc. Works great. The motors almost always sound in synch. I never notice any yaw from differential thrust.
I believe that if you are careful and use a tested system (mine is the same as what is in a single CAP) you won't have any problems.

My biggest concern is LVC (Low Voltage Cutoff). Controllers are usually programmed to stop the motor when the battery voltage drops to a certain point so it is not over discharged. This keeps you from accidently ruining your battery. You can disable this feature if you want. I think it is a much better idea to use your Tx timer so you don't fly more than 60% of your charge.

Default LVC on a Castle controller cuts off the motor at the designated voltage. Once the motor is cut off, the battery voltage rises and you can run the motor again by throttling to idle then back up. There is also an option for 'soft cutoff' where the controller slows the motor so the battery voltage stays above the minimum.

You have several advantages by the model you have chosen:
It has a relatively low wing loading
It is a kit so you can substitute wood to make it lighter - you won't need hardly any plywood as there will be little vibration.
It is 4 engine so the loss of an engine won't be as severe as a twin.
It is a bomber so you should be able to find lots of room for batteries.

I'd try to put the batteries in the wing/nacelle if possible. The pain may be making hatches to remove them.

Lastly, I am a full scale pilot. Other than a basic understanding of aerodynamics, it doesnt help much in flying RC. It can hurt if the individual is not humble enough to understand this.