Just a few quick thoughts.
From your description, it sounds as if the Tailstock is higher than the Headstock
If you levelled (removed twist ) by machining a "dumbell" you should be able to rule out twist in the bed, which we hope is not badly worn at the Headstock end.
Avoid using chucks when checking alignment. They contain their own errors which you do not want them introducing extra inaccuracies into your measurement.
It is possible that, at some time in the past, a different Tailstock, might have been fitted to your lathe, so that the centre is higher than the Headstock centreline.
I am assuming that you did check / clean the Headstock 2MT, bore and then trim up the centres before carrying out the between centre checks?
IF the Headstock is out of alignment, it means checking that there is no dirt / swarf between the Headstock and the bed proper, before trying to eliminate any error. As you already know, a minute error at the Headstock end will be magnified as you move towards the Tailstock.
Once the Headstock has been disturbed then it will need to be aligned , anyway..
To check the Headstock, for being level, you need to put a 2MT alignment g bar into the clean, undamaged bore of the mandrel. That will tell you if it the Headstock that is pointing up, or whether the Tailstock is high.
Howard