Using cellranger mkgtf w/ NCBI GFF3 files
Regarding your comment:


  This GFF file does not have the same key nomenclature as seen in
  ENSEMBL or USCS


The link you have provided corresponds to an entry in Genbank format and not to GFF format. I believe you need a file in GTF format in particular.

Nevertheless, given the fact that you have manually added the corresponding entries to the reference fasta and gtf files prior to mkref, you should have seen your gene of interest in the output. I would double check one of the original fasta headers and original gtf entries in the reference file and match these for the new entry.