did you remove the headstock from the bed? or was the headstock removed from the bed?
it's your machine, and you are free to do as you wish...but,
i would recommend leaving the headstock in it's original position, unless there is a compelling reason for moving it.
if you'd like to check and test the alignment of the headstock to the ways, you'll need a substantial piece of aluminum or machinable steel.
the larger the diameter the better, within reason.
you'll need about 10" length, but you can make it shorter or longer.
chuck it up, and indicate it's circumference so that you can have a baseline as to it's concentricity.
take a light cut (.001" or .002"deep) for an inch or so at the distal end of the rod. zero your dial. make a relief cut at 1" from the end .010" deep
advance the carriage to midpoint or a closer distance to the headstock and repeat, taking a light cut. make a relief cuts 1" or so apart for checking dimension nearer the headstock .
now that you have a prepared test bar, repeat the cut on both sites, taking a .002" cut and compare the diameter of both sites after the cuts
if the distal end is greatly smaller in diameter than the end closer to the headstock, the headstock may be out of alignment or the bed may have twist.
another possibility would be wear in the ways. all things above should be considered if the differences in diameter are large.