Re the ape studs, I had the same issue on my main bearing studs, the studs are the correct length but there is a variation in the depth of holes, I got lucky and just had to have very thin washers on 2 of them and big fat washers on the rest.
My head studs were all spot on.
Hard to imagine such a big variation as 4 to 6mm
are you sure your head or barrel is sitting on the two dowels 100% or your chain tensioner has jumped out of the groove or something simple like that
johno