Go to Advance Auto or most any other parts store and have them put a scanner on it and get the real code since P0040 isn't a good code. They'll do it gratis.

 

I don't have the tuner but from what I have read about them they are updatable, maybe try doing an update on the tuner. or try disconnecting it and see if just possibly the tuner is the culprit.

 

I'm not a mechanical expert or anything, so take my 2 cents for what ever you want. But when we have had check engine lights come on in the past the first thing the mechanics at the dealer told us to do was remove the gas cap and put it back on again then drive about 50 miles to see if that takes care of the issue.

So far every time I've seen the check engine light come on, which was maybe 3 times in my wife's old car,checkingthe gas cap did the trick.

 

Turns out I had a bad cam shaft sensor. : /

 

That makes sense now that I think about it, I had a similar issue with wierd codes being set at one time and it turned out to be the wire going to the crank shaft sensor, the wires leading to the sensor had broken loose from there loom hanger and had started to melt on the exhust manifold and would be intermittent. I was able to repair the wire and loom and wrapped it in heat shield tape I got from pace performace.