Is it possible to create a custom build and use it to view a SAM file without adding the .len and .2bit files in to the Galaxy file system as an administrator?
Yes, it definitely is.
If so, what am I doing wrong?
This is a Galaxy bug which has been fixed in this commit:
We have a release coming up, so this fix will be included in the release and will make it to our public server soon. In the meantime, note that you can use the genome fasta file rather than the len file to create a custom build and everything should work.