Hello K and Stephen,
I didn't say pins were a standard feature, just that those holes must have been the ones you used to hold down the felts against their springs when you re-assembled the spindle. The pictures are a bit hard to interpret to offer definitive opinions on, blue seems to be present over the whole surface of the bearings and with slack bolts I don't think that is a bad state of affairs.
Did you try lifting the spindle and moving it sideways to feel for any detectable slop, that would be a rather more definitive test in my opinion.
Out of interest I checked my spare spindle in the spare headstock today with just an oil film on the spindle, there was no detectable slack on either bearing with slack bolts and maybe a very slight degree of added drag with the bearing cap bolts pulled down hard on the shim stacks–it still rotated easily. Those threads by the way are 3/8 inch WHIT16 tpi.
UNC bolts are also 16 tpi but they will have the sharper 60 degree thread pitch which will not give the best fit in the headstock since the mismatch in thread angles will only allow partial contact to be made in the thread walls and the thread tips are finished differently. The UNC bolts may even be contacting the bottom of the WHIT form tappings. Try the situation with known cap bolts instead to see how things behave then; I think you will get a much more gradual degree of adjustment as a result.
The headstock fitted on my working lathe has oil cups on the top of the bearings, as well as the sprung felts and the little push fit plugs to the top up holes alongside the oil wells. One other difference is the inclusion of a grub screw in the upper side of the bearing cap to get a grip on the bearing adjustment bolts and lock them at a chosen setting. I didn't like the way they were compressing the thread on the cap bolts at those points and machined them away to allow the grub screw to grip on a plain diameter of the bolt instead
Finally, the strange bronze collar thing will definitely prevent the chuck and spindle registers from meeting as they should to properly align the chuck in its fully seated position; at the moment it is only located by the 8 tpi spindle thread and will be inaccurate to a variable degree as a result, You can't expect the lathe to do anything accurate like that so take it off, it is doing you no favours.
Regards
Brian