Elimination of smog pump/system

This is my first post, but I have read this forum for years...never really had problems till this little hiccup. I installed BBK long tube headers on my 98 cobra. When I removed the smog pipe connections from my stock manifold, the threads stripped out on all of them. So we decided to just eliminate the smog system since we got rid of the cats too. Anyways, what we ended up doing is capping the ports on the headers, and just plugging the tubes from the smog pump. Now I'm getting check engine, and I had it reading insufficient flow in the exhaust system . Is there a way for me to get around this without reprogramming my chip?

Thanks

The chip was pretty expensive because you have to go with a place that will take custom specifications, at least i'm pretty sure thats how it works. The chip was close to $500, but I had a bunch of stuff specified with flow and timing. The nice thing about it is that I can just send it back in and have it re-burned, so I will probably just do that over the winter. Alot of the chips out there can't be reprogrammed. If I find a way to fix this without altering the chip I will post it.