I think most of the BD range of cams are just reprofiled standard cams or atleast some of them, either way if its been run or turned over a few teeth out then they will touch.
As for the centre 2 pistons is that oil or carbon build up ? oil on them could be valve stem seals or guides maybe.
No worries on the manual !
I'm sure someone on here will offer some advice as I'm not that familiar with a YB although it is a engine so not a whole lot different to anything I've worked on.