First step is to verify that the head (spindle travel) is parallel to the axis of rotation, and then square to the table surface. Use a granite knee or a precision square and indicate to it with a DTI to within at least a couple .001's in the full travel. If the table is not dead flat, you may have to fudge a bit, split the difference from each side. Parallel travel should be near perfect.
I do not know if that machine has table rise & fall, or quill feed for up-down? Either way, make sure the travel is parallel to the axis of rotation & then square to the table.
These are 2 separate conditions.
To locate the pin, accurately make an arbor between centers such that one end fits the largest good collet in the spindle, and the other is a smooth snug fit in the pin socket or bearings if yours has bearings. Clean the spindle taper scupulously, insert the collet and arbor, and tighten it.
Then loosen the pin holder, carefully actuate the vertical travel (table up or quill down) and by moving the pin holder around on the loose bolts, guide the end of the arbor into the pin socket far enough that it does not wiggle. Hold in this position, and tighten bolts.
You provide no info oh how the pin holder attaches. It may be necessary to shim one or more of the bolt pads to make it perpendicular and parallel when the bolts are tightened.
Or possibly even file them.
Hopefully the adjustment provisions are easy and well made so they stay "permanently" fixed once set. Regardless, there are no short cuts.
I guess it goes without saying, the frame members should be tight and any/all gibs snugged to actual operating condition (clearance) and lubed correctly before starting the above.
smt