Things that shouldn't be.

sounds like after you had the head and block cut.....and keep in mind i know nothing about slant 6s.... one of the following has occurred

1) location dowels for the head were not reduced in length by the same amount you had cut off...or indeed their holes made deeper whichever is appropriate on your engine..
OR
2) you use head studs and you now run out of thread before the head is clamped down and the torque you see at the torque wrench, is just the nut binding on the non thread bit of the stud. use 2 sets of washers

OR

3) block or head or gasket issue something aint flat

Dave