A thread file will take care of the spindle thread. I'm not sure where this 5 thou thing comes from- the thrust surface on the SB 9 is at the other end of the spindle. I've always just pressed them on until the bull gear seats against its shoulder, and the big end of the spindle just falls where it does.
Get you a triangular file and file out all of the positive metal until you chuck will start onto the thread. A thread file may take out metal on other flanks of the thread if you can get it to cut at all. That's been my experience with them on coarse threads like this. Ken
that flange you are missing is no big deal, its only pupose it to help keeep crud out the spindle bearing.
its a press fit and if you want to add it a good lathe project, no hard rule on its diminsions except for the press fit, that .005" clearance between it and the head casting is just a general guidline, all you want is enough clearance to not rub, but not so much as to allow small chips in.
yes, to the file sugg on the spindle, if it will file, but guessing it will due to it being soft enough to deform.
as Allan noted, spindle only has one correct seating, and that is all the way.
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