I replaced the Formica on my counter top. That rod is part of the standing rigging. First loosen both turnbuckles on the forward lower shrouds. Spray PB blaster on the nut under the sink and remove nut and backing. Spray top of rod too and using vice grips under the sink so as to not scratch the rod, but not on top of any threads, clamp vise grips and use as a handle to unthread rod into that top round piece. Since it is threading from under the round piece, can't remember if it is clockwise or counter. Unthread the rod and it will then pull out of the counter top. Hope that helps. My plywood was fine, just put new Formica on it.  Made a template out of cardboard and wood slats and glue gun. Practice on Formica. I think I had to cut it upside down with a knife and then sand edges. Modern Formica is too thin to cut with jigsaw. Actually I think I used the competitor to Formica. Same stuff and thickness.