Ya gotta ask, "Why did they do that?" with the spindle plate. Maybe when it was originally put in it was so tight in the silent-blocs that the P.O. (?) couldn't turn it to align the holes and, certainly, couldn't remove it, so just cut it off to clear the primary cover.
Maybe someone here can identify those errant pegs you have so that you can put them back on eBay with the correct description. When buying all the correct parts, in addition to the correct pegs and the splined tubes (Trevor mentions), don't forget to buy the long stud that goes through the engine plates, plus the nuts that go on it. At least the stud can be easily bought.
As for replacing the swing-arm spindle, maybe that can wait until you want to do a full strip-down and rebuild, because I can see it becoming a real can of worms.
Richard L.