Thank you.
Yep, my thought was cutting an inch and some off the bottom of the head stock effectively creating a base with the head on top. Adding a rotational pin and an adjustment as you mentioned would also be added. If I slightly enlarge the holes on the base then I should be able to have the space to adjust. Now I haven't done any measuring or anything to see if I have the thickness to pull that plan off.
I'm not on that page. In my view all machines are a compromise of competing goals. If you cut anything off your bed you will sacrifice rigidity and vibration. They are too important to give away in order to achieve an improvement in axial alignment. What good is perfect alignment if you can't cut soft butter...... (gross eggageration of course).
I suspect your bed ways are fine (or at least close enough for all intents and purposes) for the size of your lathe. And assuming there is nothing between the head and the bed that is throwing off the alignment (have you removed the head and looked yet?) then I'd wager that the bottom of the head is prolly good too. It's just too difficult to accept a major flaw like that happened. If there is nothing on the ways, my guess is that the top half of the head is misaligned from the bottom half causing the spindle to point where it shouldn't.
Whether or not that exists, and if it cannot be fixed directly, I would much prefer to shim the ways as you have already done. Just finish the job. You can then go for a full repair with full length epoxy bedding if you want. But I do like what others have said about shimming, bedding, and then finish bedding without the shims.
I doubt very much that you will ever need to do this again. Therefore not much point in trying to design in any future adjustability.
It will be a lathe to love when you are done.