Best thing to do is manual.
Once you complete one forum you can copy it to other forums that you want
goto cp -permissions forum.
Don't bother with the template is was kinda broken for a long time including I think the version you are using.
Somewhere it was supposed to be fixed.
I assume the UBB7.7 versions without researching.
At Currently Editing Permissions For
select the first valid forum not template then select switch
Then review and change each permission.
It will take a while
Once you select update.
goto the right top tab Mass permissions.
Select the forum you just edited.
Then select every forum you want. with same permissions.
Then select proceed.
In fact it may be easier to copy to all forums and go back and edit forums that are different.
Then you need to review permissions site and cp.
But this is your first run so I would just worry about just yourself for now.(admin)
You really can't save the edits so when you import again all your permission edits may be lost again.
I was trying to remember about the missing permissions it could be due to during the install of ubbthreads there is a option to skip adding a admin. That you overlooked
It reads like
If are upgrading from UBB.classic or UBB.threads 6.5.x or you don't want to create your admin user now, you may proceed to create table .
But it does not import permissions from classic it just sets some defaults as I recall.