For samba3 I figured out how to tune it well. First delete /etc/config/samba. Then edit /etc/samba/smb.conf to what you want to setup.
Key features that helped my transfer speeds is to use vfat,ext3, or ext4; as NTFS-3g can be slow as it is cpu limited. When is overclocking going to be available for the G300NH????
Add this to the [global] section:
socket options = TCP_NODELAY SO_KEEPALIVE IPTOS_LOWDELAY
As for the permissions, I had similar issues. If I run my backup script, the files show up with permissions for root, and my samba use is under nobody:nogroup, so the files created in putty don't seem to be accessible, but anything I create in samba through windows has proper permissions. This worked for me, it allows me to delete, edit, add files to folders owned by root (which were created during a backup script on the router):
path = /mnt/usb
browseable = yes
user = nobody
writeable = yes
read only = no
create mask = 0777
directory mask = 0777