I was thinking about ordering the stage 2 WGA and adjusting it to work with my setup. Is this a good idea? Also, if I do this would I need to get anything else to run this?

it's fine, a lot of people are doing that. no need for anything else, although a mbc could help.

what would the MBC do to help me?

it would help enable you to control boost a little better, as well as increase levels.

Would the Greddy Profec B Spec II work for the Boost control application rather than the MBC?

yes, the profec b is a better choice imo than a mbc.