Ok well, there was no answer, but I got some advice elsewhere.
The safest method I was told of that also worked well for me was the following.
1. While in safestrap recovery with slot 1 active, make a backup of data and system.
2. Change to stock active and reboot into SS recovery.
3. Backup stock to be safe in case something goes wrong
4. Wipe with a regular factory reset.
5. Restore the backup from slot 1 into the stock slot.
7. Make sure it functions, then reboot into SS again and delete your slot 1 freeing up space.
Now I'm running JellyBeans Build 6 in my stock slot with no problems, and 19Gb free.