First off, let me state that I disagree with all the people who talk about squirrel substituting for chicken. While many recipes are interchangeable, squirrel has a totally different flavor. The are only two game meats I know of that truly substitute, one-to-one, for chicken: Rabbit and rattlesnake.
So, you could, for instance, do a squirrel fricassee, which would be delicious. But it would not taste like the same dish done with a chicken.
That said, let me take your questions in order:
1. I don't think that squirrel and tomatoes particularly compliment each other. Only three of my many recipes for preparing flagtails use tomatoes, and each of them is some form of stew. I've a Brusnwick Stew version, a jambalya, and a hunter's stew. That's it on squirrels mixed with tomatoes.
Shooting from the hip, I can see where squirrel and fried green tomatoes might pair nicely. But I haven't tried it, so can't say for sure. For instance, you might strip cook meat from the bones. Combine it in a brown sauce of some kind, and serve that over the fried green tomatoes.
2. #squirrels:chicken. Depends a lot on sizes, of course. But as a rule of thumb I'd say two-three Fox squirrels or three-four mature Grays.
3. Why are they eating your tomato vines? I dunno! And you can quote me on that.  | 
