I just spoke to Scott @ MRT, and he said that the hood has gone back to the tooling phase where they are working on an underhood "cabinet" to seal the current air box. So to answer the main question, yes this hood will be taking the stock designed CAI into account. He hopes to have engineering sign off on the hood by late next week and begin production/sales shortly after. This hood will work with the MRT hood struts as well.
Also, he confirmed that they are working with SilverHorse Racing who is providing the quarter louvers for their Reload package.
Also, he confirmed that they are working with SilverHorse Racing who is providing the quarter louvers for their Reload package.