I have a set of 2 1/2" (measure out to 4", however) Drag Specialty risers and they were drilled all the way through. Were yours threaded? Mine were not and I had to purchase four longer bolts and blind nuts.
The holes were somewhat clogged up by the powder coating. Might this be your issue? The nuts were a tight fit into the hex holes and I can well see excess powder blocking and acting like you were busting through metal.
For what its worth, I did not use them on my FXD as the pullback bend combined with the bend in the speedo housing placed the speedo too vertical. I'll be listing mine for sale soon.
Good luck. You just might need longer bolts, blind nuts, and a cleanout of the holes.