Dial a 1-2-3 block in true with your X axis, then check it along Y. No need to make any cuts - eliminate that variable from your testing to get started. It may actually be easier to tram your vise in, then check with a 1-2-3 block, but that does add the vise into the equation.
Additionally (and backing up a smidge) When you finish tramming did you run a single indicator across your range of motion? (Actually 6" should do). One downside to the SST kind of tool is that it's easy to get confused and have one indicator reading +0.002" and the other reading -0.002", which can look great, but really indicates a 0.004 offset. Sweeping a single indicator as a final sanity check eliminates this possibility.
GsT
Additionally (and backing up a smidge) When you finish tramming did you run a single indicator across your range of motion? (Actually 6" should do). One downside to the SST kind of tool is that it's easy to get confused and have one indicator reading +0.002" and the other reading -0.002", which can look great, but really indicates a 0.004 offset. Sweeping a single indicator as a final sanity check eliminates this possibility.
GsT