If the space between the fork and the slave cylinder is a little tight to get the rod in with some clearance for adjustment I would consider some type of spacer between the block and the slave cylinder bracket rather than removing the spacer from under the fork pivot bracket in the bellhousing. You want the fork spaced pretty well forward in the bellhousing opening so you don't run out of clearance for full travel.
I'm curious why ERA supplies that long, built up rod nut on some builds and just the acorn nut on the end on others like mine. I guess I have clutch rod envy.