That style of turret is usually designed to suit a particular height of tool – inserted tools should be accurately made to put the insert on the correct height so the tools just required clamping into the turret to be on centre.. The only time shims are usually used iis if, say, a 12mm tool is used in a machine designed for 16mm tooling, where a 4 mm shim would be required. The manual should state what size tooling the turret is designed for, and using this size tool should put it on centre.
When the turret is initially fitted onto the machine, it should be adusted so that a standard tool is correctly on centre, but a bump (i.e running into the chuck) can easily knock the tool disc out of alignment. You can check for this with a dial gauge running against the tool bottom seating faceon the tool disc – this should be parallel to the X axis motion. If the disc has moved, it will show a taper . The rear vertical face should also be parallel to the X axis motion – the whole turret body can be displaced in a bump
You would have consult the machine documentation for how to remedy this. On the industrial machines I used to work with, the disc was usually positioned with a Hirth coupling, located with taper pins. A bump would rotate the halves of the coupling, damaging the pins & causing the disc misalignment. The cure in this case was a strip down, remove the damaged pins & stone the flat surfaces to remove any burrs. The halves of the coupling had a "master" taper pin hole that re-aligned the coupling halves correctly. With this in place, the location pin holes were re-reamed, new pins fitted and, most importantly, the "Master" pin removed before re-assembly.
I don't know how the Boxfrod turret postions, but I doubt it will have a Hirth coupling – for cost reasons if nothing else. Given it is intended for educational use it would be reasonable to assume that collisions would occur & have have a straight forward means to sort out any misalignment – the four central screws could, for example, just be a friction clamp that allows the disc to slip easily & re-alignment as easy as loosening them, clocking the tool seating face parallel with the X axis motion & re-tightening.
I would havce expected the drill / boring bar bores to be out in this case, though. If they are truly on centre (clock the bores with the X axis in the X zero position) that would suggest it is your tool holders that are not accuarte enough WRT to tip height from the tool shank base.
Nigel B.