The stones each have their own box (Dan’s Whetstones sells them that way if you don’t have the patience to make your own) so if I need adjustments per stone, I’ll just change things on the appropriate box.
I thought about a stop on the front, but then put in two different gouges and needed two different heights in the vise because the gouges are slightly different lengths. That will only get more pronounced with time, I expect. So lines seem best.
If you go to Dave Fisher’s original page, one of his readers made a jig for putting the gouge in the tormek short tool jig, which seems like it might be useful, but I’m going to use it for a few months putting the gouge as far into the jig as possible and see.
As for flex, I’m not putting any force into the rod, and a 3/8 stainless rod doesn’t flex much anyhow. But all of the force should be side to side, not pressing on the stone or rod. 3/8 is more than enough, but if you’re a gorilla, use 1/2 inch stainless rod.