clearing codes
I have had similar problems clearing codes. I tried the disconnect batteries, disconnect connectors behind air cleaner etc but to no avail. Even tried going to Auto Zone and having them try to read and clear codes (they have a unit and are usually nice enough to try for no charge).
I ended up getting the software and cables from Harison. It runs on my laptop and allows you to read, monitor and/or clear codes. This finally worked for me. The cost is in the one hundred dollar range for the software and necessary cables etc.