The machine shop guy is correct, the stem on your CB is welded as are most other CB models. The GSXR trees are aluminium and I think the stem is also. Not a good idea to bore the CB trees as you won't have much meat left if any at all.
What I would do is measure up your stock CB stem and machine a new stem in stainless or 7075 aluminium and press this into the GSXR lower tree, this way you can machine the new stem with the extra length probably required for the extra thickness of the GSXR trees.
Or you could remove the CB stem by grinding the welds etc, check the diameter to see if it's compatable with the GSXR tree, if sizes look good then you can press the CB stem into the GSXR tree, you might have to bush the tree as I would imagine the GSXR stem being a bit bigger, but it might be too short at the top if the GSXR upper tree is thicker.
ALL IS POSSIBLE. Greg at Ohio cafe racers has fitted a GSXR front end to his CB350 twin.
Kevin.