For rust on the tubes, jointer surface, the black bars on the casters, etc, I use Mothers Chrome and Aluminum polish. I get it at one of the auto parts stores, Checker, I think. Use a Scotch Brite pad.
Unless you're a fan of dull gray metal, never use naval jelly.
If the tubes are really rusted, you can resurface them, but I'd only do this if the above fails. Use 320 grit wet dry sandpaper (auto parts store) and the Mothers. Keep it wet and work the sandpaper like a shoeshine rag, keeping the swirls perpendicular to the tubes as opposed to parallel.
If you have rust on the bottom of the Mark V's legs, I would put some cardboard on the floor, put the main and extension tables at the same height, then flip the Mark V upside down so it's legs are sticking straight up, kind of like a dead horse. Take the casters off so you can really go after the rust with sandpaper. After you get it all, use the touch up paint Shopsmith sells. It will perfectly match and you'll be like brand new.
PS- A few years ago, I bought, refurbished and re-sold about 35 Mark V's as well as hundreds of SPT's. What I'm sharing with you above was learned the hard way.