What oversized valves are you using? The entry level 6000 Ferrea valves have a known problem (unless very recently purchased/manufactured). There's a material incompatibility problem with the Yamaha head. Basically the 3S valve seats are too hard & lead to deformation of the valves. Given your intake valves are the ones affected, sounds to be the issue to me.
If you do have Ferrea valves, I believe they'll replace them free of charge.
Edit....Oops, didn't read the last page. Head's coming off buddy.