If I'm understanding you correctly about the back end, your scales will extend past the end of the tang so there is a gap between them after the tang ends. You could probably get away with filling it with epoxy, but the neater approach would be to put a peice of matching spacer wood between the scales. If you want to make it fit really well, I would cut out the spacer oversized and thicker than the tang, then fit one edge of the spacer to the end of the tang. It should still overhang the sideview profile on top and bottom and on the backside. Now temporarily fasten one of the scales to the tang, flatten one side of the spacer, and epoxy it in position to the scale you attached. Once that's dry, you should have a spacer that's thicker than the tang stuck to one scale. Now lay down the tang with your attached scale facing up on a flat sanding surface and sand down the extra thickness of the spacer until its flush with the tang. Now glue up the other scale, and once you trim the top, bottom, and back you should have a pretty seamless joint on the back. This probably sounded much more complicated than it actually is.
Also, not sure why you want to use JB weld. It's a bit thick and dark, so it doesn't make the nicest looking glue lines for this type of work. 60 minute 2 ton epoxy from the hardware store works great. Just be sure to clean up the tang with coarse sandpaper to remove scale/rust and degrease the scales and the tang with acetone or other solvent just before you glue it up. Once the epoxy is cured the BLO will not affect it, probably wouldn't affect cured JB weld either (since it's epoxy as well).
Threaded rod for rivets is interesting. You said you would peen them over 1/4" washers, what kind of washers? The standard 1/4" flat washer has about a 3/4" diameter which is a massive countersink on a knife handle. An AN washer would be better, more like 1/2" diameter.
If you go to ACE hardware or maybe Home Depot/Lowe's you can find aluminum, stainless steel, and brass rod or tube (not threaded) of various diameters, most likely including 1/4". Then you can pin the scales, no countersink or peening required, and trim them flush. That would be a much neater look. The epoxy is plenty strong if you prep the surfaces correctly.