I'm not sure what would have caused the light to flash or the engine to surge. I think mine surged a little bit when I flipped the lid and the engine was cold. I've tried flipping the lid, but can't really say if it improves performance or mileage. The one thing it definitely does is increase the noise from the intake when you really get on the gas. The biggest factor I've found in mileage thus far is outside air temps and the number of heat cycles the engine goes through per gas tank. I've been religiously calculating mileage on each fill up since December. My truck is in tip to running condition despite its mileage. What I've found is that the worst mileage occurs when I do a lot of short trips, with cold starts, in cold weather. My mileage drops to about 14. Last week, I did a mix of short and long trips, and the outside temps were much higher than they were in December. The difference in warm up time when it's 25 degrees versus the time when it's 65-70 degrees is huge. At 25 degrees it takes about 4 miles to get up to normal temperature. At 65-70, it takes about 1 to 1 1/2 miles. That's a tremendous difference.
Back to the filter cover. We know that the snorkel from the fender to the filter housing is barely suitable. At the same time, it is a "cold air intake." But the cold air is heated by that valve on the snorkel that pulls warm air off the exhaust manifold. Every time you get something good, you get something bad it seems.
1. A cold air intake that's too small in any condition.
2. An open air filter element draws in the hottest air possible in warm weather.
3. An open air filter element in cold weather may cause the engine to take even longer to heat up which may reduce your mileage even more.
4. The valve on the snorkel helps the engine heat up on the stock air intake. Unfortunately, most of them never work properly. They seem to be either closed fully, or partially open. They never fully open. So air intake is further restricted.
On mine, I leave the cover in the proper position. The only change I made was I removed the valve/wax pellet assembly from the snorkel and sealed the hole with that tape that's like aluminum foil with an adhesive backing. With the warmer weather, I'm seeing 16-17MPG. I don't think it will get better than that.