What you are saying is to jog the robot to the coordinates of the tool frame or the user frame? IF the coordinates relate to a position in space IE a pin. Than switch to joint mode and jog the robot to the tip of the 'point'. Than take the values from the joint cord system and calculate the differences than jog the robot to the Vernier marks and re-master. But where would I input the differences that I calculated. I'm gonna send you a PM maybe you could call me to explain in detail if you wouldn't mind 
Go to your frame screen, Enter the frame you want and write down the Direct Entry coordinates. Now create a program and inside declare a point anywhere, doesn't matter but ake sure you use the correct UTOOL and User Frame 0 (UF0), and change its coords to the frame coords. Move there. The robot should now be close to an identifiable reference point. A point someone (the integrator or a programmer in the past) used as the frame reference point.
Open the point's position data and change the representation to joint. You should now see the joint angles of each axis for this position. Write them down.
Now switch your jog mode to JOINT and try to correct the position of each axis separately so that the robot tool is aligned and touching the reference point. You should be carefull as to not correct one axis too much but better spread the fault difference by applying small corrections to every axis.
Now when you are done and you have aligned the robot with the frame reference point, declare another point in your program. You should now have 2 points: point 1 is the original point from the Frame Coords used as direct entry and point 2 is the modified version of it in order to touch the reference point.
Write down the JOINT angles of each axis for point 2 and calculate the difference. You should come up with a result of minor degree difference for some axes or all of them negative or positive, the difference margin should not be large. If it is large something has gone wrong.
Now, put your robot axis to ZERO position and using the results from your previous calculation apply them to each axis. Again, you should check to see that after applying the correction to each axis the marks are not way off of where they were supposed to be, it should be +-2 max 3 degrees. If the Vernier mark is visually way off then something has gone wrong. When you are done applying the corrections, master your robot with zero mastering, Calibrate and you are done!
Repeat the procedure by moving to point 1 (the frame ZERO point, not the corrected one) and verify that the robot now correctly aligns with the frame reference point by using the direct entry values.
Things that can go wrong:
Identifying and using a reference point that is not a good reference point. (worn out, or with excess tolerance due to wear and tear or age).
The frame may (and most propably) has been set when the system was brand new and before any tolerances to the system's parts were introduced due to normal aging and wear. The same goes for the mechanical parts of the robot. Machines age, and as they age new tolerances are introduced and we copensate our programs to correct any faults due to aging.
If you come by any of these possibilities, remaster to zero as before using the marks and your eyes and just reteach the user frame. The tool frame does not need to be taught, you can use the direct entry values.