Yes, that muffler is reversible.
Yes, you will need adapters if you don't have a 2.25" or a 2.50" pipe depending on how you want to install it.
No, there should not be a problem with accepting 2x 2.25" and going out with 2.50".
Yes, you can use this muffler to eliminate the entire Y-pipe if you have one. I think R50s already use a dual in single out muffler that eliminates the need to use a Y-pipe.
If you want a glass pack, that Magnaflow is definitely better than Cherry Bomb.
You can also use that muffler as a pre-muffler and then add another 2.50" in/out muffler for more quietness.
Good luck with your purchase!