Any question answered...

I have a road bike wheel equipped with a shimano hub. The hub is missing the innards & freehub.

I was wondering if I simply purchased a new shimano road hub, that I could transplant over the freehub, axle, cones & bearings to the old hub?

I need the hub to fit into an older road frame (126mm spacing I think) are new hub axles the same length? Are the cones & bearings the same size?

Your problems are twofold - first, all the current freehub bodies are too wide, and second that if your hub is old enough to have been made for 126mm OLN it won't accept a modern freehub body. Also current axles are too long, although that's a trivial issue next to the other things. Show us some pictures, I've got some unused Shimano hub guts left over from Fixxer conversions and can sort you out with parts, but you're almost certainly going to end up with something 130mm OLN and will have to spring the frame.