Myford 7 series headstocks have alignment blocks underneath. They were hand scraped at the factory to give the correct spindle alignment so that the lathe produces faced surfaces that are slightly concave
The spindle axis should also rise at an angle of about 0.002" in 12" as you go down the bed, so as the bearings wear, the lathe wears Into accuracy before it wears out of accuracy.
As Pete Rimmer has noted, you'll need to check that the tailstock aligns correctly, it should also be angled slightly upwards to allow for wear.
If you need to correct the elevation of the tailstock, it's probably going to be faster and safer to make a new base section and scrape it to the correct height and alignment, than it woutdoor be to risk messing up the headstock casting. You could also mill down the underside of the base section, stick turcite onto it, and scrape the turcite to get the correct alignment. Turcite works like the mythical "putting-on tool".
There were two guide systems used for the saddle.
The earlier narrow guide, that guided only on the front shear of the bed, and was prone to rapid wearing
And the later, Radford inspired, wide guide, which guides the saddle on the front and back of the bed. On the wide guide, the little projection in the middle of the saddle, is relieved, so that it does not contact or wear the inside of the front bed shear.
The saddle should align so that the cross slide travel will result in the lathe cutting a faced surface that is concave at an angle of a couple of thou in a foot.
The bearing surfaces for the cross slide were hand scraped both for fit and for a smooth moving (no stick-slip motion). It is usual to scrape the surfaces to give fewer spots in the middle of the dovetails on the saddle, so that the cross slide maintains contact at the end of the dovetails as wear takes place.
You will probably have to fiddle with the packs of shims to set the correct clearances between the saddle and the bed
And also fiddle with the position of the apron, to get the half nuts to align properly on the leadscrew and the pinion to mesh correctly with the rack.