Bisonfan, I'm glad to hear that things are getting better with your lathe :)  One thing that I hadn't asked before was how you are measuring the alignment of your chuck.  What I recommend (and you might already be doing this…) is to get yourself a piece of ground steel shaft from a printer, the thicker the better (if you can find an older line printer, you'll get 15mm diameter or larger shafts).  These are about as round a shaft as you can find, and bloody hard, so they will stand up to a lot of rechucking without getting marred.  Chuck up a piece of that shaft and mark out (with a sharpie) distances every couple of inches or so from your chuck's jaws.  Next, use a DTI to measure it's eccentricity from the lathe's spindle axis at different distances from the chuck.  This will give you a very accurate measure of the chuck's alignment.  Note that you will measure both the headstock alignment (the mean of the DTI readings), as well as the eccentricity of the chuck/chuck-mounting (max-min of the DTI readings).  If the max-min is constant as measure further from the chuck, then the axis of the chuck's jaws is parallel with the spindle axis.  If the chuck's jaws are not parallel with the spindle axis, then the max-min will INCREASE as you get further from the chuck.

-Chris

What you do depends on where the problem lies.  Is the front of the chuck parallel with the back of the chuck?  With a cheap chuck, it's conceivable that some crap got underneath the chuck with the opposite face was being machined.  I had some tooling – I can't remember what – where this was the case. 8" is plenty long enough for the steel shaft, though, as long as it is accurately round (that's why the ground shafting is ideal).  1/2" diameter is thick enough that it won't sag enough to matter under its own weight.

In a 3-jaw chuck, the key surfaces are the slots in which the jaws slide, and the rear face of the chuck.  If these are parallel, then your chuck is fine.  The other things to check are the jaws themselves.  Do the jaws have any play when mounted in the chuck?  Are the jaws' sliding surfaces (those that slide in the slots of the chuck body) at right angles to the jaws' clamping surfaces?  If the jaws fit well into the chuck body and the jaws' clamping surfaces are at right angles to their sliding surfaces, then, if the problem is with the chuck itself, it must be either the ways for the chuck jaws or the rear surface of the chuck.  Beyond that, it would have to be the mounting plate of your spindle.

Keep in mind, though, that your tooling has to be more accurate than what you plan to make with it.  Rebuilding a defective chuck isn't rocket science, but it requires very careful measurements and accurate machining, maybe even scraping.  At some point, you need to ask yourself whether or not it is worth it to repair the chuck (that is, if it is damaged).