I like this thread already...and it's just starting...
So the big offender here is the fuel pump - and it looks like you are well on your way on that. There's a 90% chance you might be able to clean and reuse the entire unit...except for the screen. I doubt any rust made its way into the fuel line, but you may want to inspect and blow it out with some compressed air.
Next is the tank. Kreem makes a line of products designed to clean/prep the tank and then protect it. The prep product eliminates rust. Here's a link...you can get this stuff from most moto (on-line and in-store) retailers as well as Amazon.
https://kreem.com/tankprep.html
If you haven't cranked it over yet - don't (I assume the dead battery kept you from that anyway). I would remove each spark plug and put a teaspoon or two of light-weight oil (Marvelous Mystery Oil) into each cylinder. This will save the cylinders if there are stuck rings. Let the MMO sit in the engine a few days. Hook up your new battery and crank the engine for 5-10 seconds. You will want to put an old towel over the head because that MMO oil is going to go everywhere. Reinstall new plugs and make sure the caps are seated well.
Don't change the oil yet. Do that after you get the bike started. You don't want to crank this thing over, and prime the oil system all at the same time.
Remove the TB intake boots and spray some carb cleaner into the throttle bodies as you exercise the throttle. This will prevent a stuck throttle situation.
Take a good look at your tires...and check the date. At 10 years old, I would not feel comfortable riding them because they may feel like you are riding on ice as you apply power or enter a turn a little hot (as the tires age, they become hard and don't deform under load).
I would also suggest a coolant change as well as flushing the brakes. Not a lot of effort, but can save you from some real headaches.
I'll think of more things...I have to run into a meeting...
BTW, where in NJ are you?