How to get total pm10/pm25 from cmaq v5.4_isam output

Yes, you can use these cutoff variables from the AELMO files. For the aggregation of the individual PM species to total PM mass, you can use the SpecDef files released with the previous version of CMAQ (CMAQv5.3.3) as guidance. You may also find the related discussion in this other recent thread helpful.