This earlier discussion may be helpful.
In short, the issue seems to be that the MEGAN emproc program does not know how to handle the VGTYP “-9999” token value used by convention in MCIP when the hybrid vertical coordinate system was used in WRF. emproc likely was coded before this convention was introduced in MCIP5.0
I do not know why emproc looks for VGTYP and what if anything it might be used for in the actual MEGAN emissions calculations. You would have to examine the emproc Fortran source code and then update it to handle the case when VGTYP is -9999.
Or starting in CMAQv5.4, you could make use of the MEGAN3 inline capability instead of trying to run MEGAN2.1 offline via emproc. This was noted by @willison.jeff in the earlier thread you started, pointing you to a previous discussion about the much simpler workflow needed to accomplish this.