OP here. Today I put the OEM filter back in, used some grease to hold the metal plate to it (thanks for the tip), and finally got the %&$@# air filter cover in place. The protruding screw and nut on the bottom of the airbox made it a royal pain to get things in place.
After that I took the C5 for a 15 mile jaunt on the highway in front of Seattle's waterfront and into West Seattle. The backfires were less than usual, but still present. The motor felt strangled and not willing to rev.
Back home I took the airbox cover off and removed the OEM filter. I put the K&N air filter back in and didn't put the airbox cover on. After securing the outer cover I rode the same route as before. BIG difference! The motor could breathe again and had more pull at all rpm's. There were more pops and poots but with the performance increase, how could I care? Besides, the shop is (hopefully) going to map the fuel/air and get a power commander working on it.
I like the cone filter with welding that Shappers/r80rt did. But I would rather have a K&N filter that properly fits in place of the OEM filter so that the airbox cover will properly seal the airbox.
I think someone mentioned using black electric tape to discretely seal the airbox on black C5's. I might try that tomorrow.