Hi @Jeff
The Gencode GTF with the headers removed will work with every tool I can think of. This is where I would expect it to be sourced. Note that the GFF3 might work with some tools but not others.
These will be “a match” with the UCSC hg38 reference genome indexed at the UseGalaxy servers. Removing the # header lines that data providers include for provenance are usually better removed to bring the file into strict GTF specification.
This guide explains more details about pairing up reference data, using this assembly as an example.
Please give that a review, and you can ask more follow up questions. We’d like to get this working for you and it all seems to be very close given your updates! 