[LS short box]

I've done a number LS swaps with junk yard engines and totally rebuilt engines. If you gojunk yard I'd have them pull the valve covers to if it's clean and if it is it means the oil has most likely been changed regluary. Also a compression check will tell the tale on ring seal and valve seal. If you purchase used I would replace the timing chain and oil pump. If you plan to rebuild something I would buy a 6.0. Iron block engines are going to cheaper than aluminum block engines. Doesn't cost more to build than a 5.3. If you get a later model 6.0 it will have the better L92 heads. If you decide on a bigger cam you will need new valve springs and push rods. I've used the LS7 lifters on rebuilds. I have the front alignment tool for the front cover. Before I had that I used a buddy's front balancer that he honed out slightly so it would slip over the crank to align the front cover. Use the feeler gauges to align the oil pump. Rocker trunion upgrade? All depends on engine mileage. Hate to have a bunch of tiny needle bearings in the engine? New rear seal? I would.
I like doing things right and doing it once. Not a fan of putting a engine in and then have troubles with it. Kind of takes the fun out of a project.
Good luck with your project.