Good, another problem diagnosed! Wiper fluid reservoir. Now on to something a little harder to diagnose based on the description. I'll throw a few things out.
First, you should not get a CEL when the ECM is trying to learn. What you would probably experience is roughness on the road when you were accelerating, etc. But no CEL. I think it would be worth letting the CEL come on and stay, then get the codes read (somewhere like AutoZone, etc). Bring those codes back and perhaps we can scratch our heads some more.
As far as the sounds in the cab, could be anything you're hearing. Could be a exhaust manifold leak (you mentioned they did heads, etc.). Also, if she's having trouble at higher rpms, could be something to do with fuel delivery (filter, spoiled gas working it's way thru, etc.). Let me throw this out to the forum since it's been sitting for 9 months. Seafoam?