Ian,
Let me say at the outset that I’m not familiar with Raglan lathes however I would make a few suggestions which would probably apply to lathes in general. Some of it might be obvious and if so I apologise for teaching grandmother to suck eggs!
1) You say you have clocked (used a DTI) on what I presume is the register for the chuck on the spindle nose and on a centre placed in the morse taper of the spindle. There is a danger of introducing error by clocking on a centre in these circumstances; it would be safer to use the clock directly onto the inside of the morse taper if at all possible. If there is any muck or a bruise between the male and female tapers it will throw the centre out and show up as eccentricity.
2) Are both readings of eccentricity in the same place? Mark the spindle nose with a bit of felt tip and make sure.
3) Are there any bruises on either register or the inside of the morse taper?
4) You say the bearings are “tight”. I presume you mean there is no end float along the length of the spindle. Are they bronze bearings or needle rollers/ball races? Are they in good condition? Before you make any decisions I would strip and clean the bearings and make certain that there are no obvious problems with roughness or wear here. Reassemble and try the spindle nose and bore using the clock again.
I cannot see any misalignment of the bed affecting the eccentricity of the spindle nose personally; even if it it was so bad that it was putting a twist into the headstock I cannot see how it could make the spindle run eccentric for the type of checks you’re undertaking.
I undertake machining for a living and agree with what Steve says about cost; it would not be a cheap option to have a new spindle made but it might not amount to that.
Just as an afterthought, I appreciate that 0.002″ run out seems excessive but are you sure that is was not manufactured that way? As an example I’m in the process of altering an old Zyto lathe bed and cross slide to make a grinding rig for a job and the cross-slide was 0.010″ out of square across the bed both vertically and horizontally; there was not a significant amount of wear so it must have been made that way. It’s now been corrected but I was amazed that such low standards could have been deemed as acceptable!
Sorry if I’ve waffled but I hope this helps.
John.