Yes, you can modify nearly any fasta files to create a custom genome/build. For your case, both source fasta files must be loaded into your history first. Make sure the formatting is exactly the same with NormalizeFasta before using Concatenate.
The source for the locally cashed mm9 genome is UCSC (Downloads area, http://genome.ucsc.edu). Download locally from UCSC, then upload to Galaxy using FTP.
Thanks, Jen, Galaxy team