Copper RTV spec sheet says this about that:
"Chemical / Solvent Resistance
The product retains effective properties in contact with most shop fluids, automotive fluids, such as motor oil, transmission fluids, alcohol and antifreeze solutions. Note: Not recommended for parts in contact with gasoline."
If the joint was tight to begin with, it should be hard to get -anything- in there, so...
I'd be wary of spraying anything to check for leaks. Small ones the computer will correct faster than you can notice them...big leaks tend to stand out on their own. A smoke test finds them all. You can rent a smoke machine from your local partysRUs, but hey...whatever works.
I think 3-digit codes are found w/late model, but you have a chip/tune, so...
My opinion at this point is you have a combination of vacuum leaks and electrical issues. I'd go after vacuum leaks first. Just remember that vacuum leaks are unlikely to throw CID errors.