So... basically you got rid of the ribbing. Hopefully that ribbing was 1) not structural, and 2) it wasn't there to keep the flow from being laminar.
Turbulent flow>Laminar flow (velocity wise).
My suggestion would be to get rid of the box entirely and start from scratch. Design a box and ducting that would pull in cool air without issue, and still have better flow characteristics than stock.
Something to consider when modifying the car's stock equipment:
1) Design is dictated by 3 things for a mass market.
a) Cost to produce (Material, Tooling, etc)
b) Reliability/Endurance
c) Performance
Choose wisely which one you choose to modify in order to increase the other two.
I bring that up for a simple reason: What you're doing is removing those ridges for a presumed "better" air flow. The trouble is just by logic it doesn't seem to me that it will based on the above.
Cost to produce: Mazda had to produce that intake box, it had to spend money to produce it. What would cost more? A simple box with internally smooth sides, or a box with ribs spaced throughout the interior? If you answered the internally smooth sides, you'd be right. The molds for such a box would be made (tooling cost) relatively simply, with taking a plate and machining the exterior surface to match perfectly. Consequently the stock box is not like that? Why? Do the engineers that designed it know less than we do today? Probably not. In which case there must be a reason for those ribs.
The long and short of it is this: You have basically taken a golf ball with dimples in it and filed the rises down to create a smooth ball. This animation shows how the dimples work:
http://www.livescience.com/common/me...olfBallScience
(sorry for the dreamy voice the guy has)
Something cool:
http://www.ebaumsworld.com/video/watch/80521365/