IOF, I'm thinking your re routing of wiring is getting a little complicated... Back feeding the breaker box keeps things simple, but its not the "politically correct" way of doing things. You might consider this since it would give you the option to turn any breaker on that you want. If its not your cup of tea, perhaps another reader would benefit..
I have a portable generator that can maintain 5600 watts and can take 8300 watt bursts. Since it has a 220 volt out, I have mine wired directly to the breaker box by back feeding it thru a 220 breaker. This is the hill billy way of doing it verses having a seperate sub panel installed by an electrician. Back feeding the generator thru a breaker in the breaker box can be done safely as long as you KNOW what your doing. There is a specefic sequence of turning breakers on and off that must be followed so that there isn't a problem. Here is how I do it.
1. Turn OFF the MAIN breaker to the house (most important)
2. Turn OFF all breakers in the box
3. Start the generator
4. Turn on the breaker the generator is back feeding thru
5. Turn on the breakers in the house you want power to (be selective not to over burden the generator)
Its most imperative the Main breaker to the house is OFF while the Generator breaker is ON.
When you first install this type of set up, you will need to check voltages with a volt meter in the breaker box (before turning on any breakers) to be sure its working properly.
There is mixed opinions on powering sensitive electronic stuff with a generator for example computers and LCD tvs and whatever. I've never had any issues.
I recently ran this set up during an outage for about 8 hours, worked fantastic! Even thru on the hot water tank for a while! And I was able to run my 220 volt well pump to have water
Its important to rotate power hogging appliances though...