SMB: auto-unmount then unable to re-mount without restart
I'm going to put up an answer to question 3. Not sure the rest can be easily diagnosed.
"If an auto-unmount occurs, how can I re-mount the directory without restarting?"
Try diskutil umount /Volumes/josh and it should do the trick.
The "File exists" error is showing up because the mount point it wants to use is already present. Looks like the disk isn't actually unmounted, just that Finder can't see it. This is why Matlab can still access the files on it.