Hi David,
According to the log file, the WRF version was 3.8.
ESM - can you try using the latest release of the two-way version that is available from the CMAS Center Download site under the CMAQ v5.3 page. CMAQ version 5.3 Release (August 2019)
Please download and try the WRFv4.1.1-CMAQv5.3 Tarball
Thank you,
Liz