Tried many ways and found out the issue lays in the 9.3 freenas.
Ran it in the same jail and it doesn't work correctly because permissions need to be changed for writing and access if any changes are made.
The problem is any permission changes in any plugin cause the plugins to no longer work in 9.3 even if its merely increasing them.
Now if you happened to have set this up before the 9.3 upgrade you ok but installing after is a mess and frankly a massive headache not worth dealing with.
Hell even transmission can't download to the folder you set it two because it doesn't have permission even if the change before starting is as small as this /mnt/media/downloads/transmission/complete/tv.
So you have all these options to change or set folders but you can't actually do this because of lack of permission.
it is possibly to get everything setup on FN9.3 using either the same jail or different jails. I maintain I post on my blog that explains how I do it. but, this is with sabnzbd + CP, and automatic post-processing using nzbToMedia. if you're interested Google "jruehlig freenas"
heres a few suggestions if you choose to not follow my guide.
* running them in different jails doesn't solve any permission issues, even if they can access the same files, they still see what UID/GID owns the files
* you're on the right track with not changing permissions/ownership of your jail datasets. instead mount a dataset for your downloads+media into your plugin jail(s). you can change the permission level/ownership of this dataset.
* transmission and SR both need to be able to write to the files. either..
1) run them with the same user
2) put user 'media' and 'transmission' in a common group in their jail(s). make transmission write the files as group writable (77x)
3) have transmission write files as world writeable (777)
only option 3 requires no command line steps. I use option 1 in my blog post