Cheech,
Number 1......Run it with no cowl to see if it runs OK before you go any farther.

If it runs OK go back to the baffle system AND put a baffle on the top opening (of the baffle you show), extending that baffle from the front to the firewall, next put a baffle on the lower part of the opening to direct the flow of air over the head. If you dont have these inner baffles the air enters the hole and flows down to the bottom openings without passing over/thru the cyl & head.