Hi @daikez,
regarding your first question, you can generate an Augustus model by using the Augustus training tool.
Respecting the following questions, if you pretend to re-annotate the rn7.2 assembly, then it is not a good idea to use the protein.fna and rna.fna datafiles from the rn7.2 assembly because that information has already been used for performing the annotation, then it won’t provide any additional information.
You can get an updated EST dataset from Genbank. I recorded a short video about how to get the sequences.
On the other hand, the protein sequences can be obtained from UniProt.
Let me know if you need additional information.
Regards.