Nige,
Once you have cleaned up the 2MT taper in the mandrel, BY HAND, you can fit your new 2MT Alignment bar.
Then, having mounted a D T I in the Toolpost, you set the clock on the centreline of the Alignment bar, before running the saddle up and down the bed.
As you adjust the position of the Headstock, the difference in readings between Headstock and Tailstock end should decrease until, hopefully, you reduce them to Zero. This will be a matter of checking, adjusting and rechecking again, and again, until you can get the Zero difference more than once.
Once you are certain that the Headstock is aligned, you fit dead centres (in good condition) to Mandrel and Tailstock, and with the Alignment bar held between centres, you start adjusting the Tailstock in like manner.
If your centres are obviously damaged, you mount each one in the now pristine 2MT Mandrel, in the freshly aligned Headstock, offset the topslide to 30 degrees, and clean up the centre. Repeat for the second one, before starting the Tasilstock alignment, as above..
The only time that you need the Tailstock off the centreline, is if you wish to turn a long taper. Short tapers can be produced by offsetting the Topslide.
HTH
Howard