Because of relocating the spring perches and shock mounts, and changing around the hard lines due to my disc conversion, I have the screw holes in the rear axle. What do I plug those with?

On the one side, it's the hole from the brake line junction box fastener, and I assume I'm putting that back in where it was.

On the other side, it's the two holes from the hard line bracket, and I'm not reusing that. According to advice, I'm welding on two new tabs to hold those...

 

Put a screw in the hole or weld it shut

 

I don't think the screw holes will go all the way into the housing. Are you worried about oil getting out and water getting in?

 

Every axle I've worked on, the holes do indeed go all the way thru the tube....too much work to do a blind hole vs thru hole

Just put a screw with some RTV on the threads in it....or weld it up since you're gonna be welding on some new tabs anyway.

 

Even with my disc brakes I still used the hold down to hold the hardline. And on my Comanche that's spring under I still used that bracket for the hardline.