T56 trans with Clutch, pressure plate, flywheel, necessary hardware: $2000
Hydraulic TO bearing: $150 - Generally still needed with an LS1 swap...
Starter (most truck pullouts don't come with them): $100
Fbody 6-speed Harness & 0411 PCM: $400 - Not needed at all
Fbody LS1 Intake Manifold w/injectors, TB, Sensors & bolts: $180
Fbody LS1 Oil Pan, Pickup, windage tray, gasket and bolts: $250
Fbody LS1 Water Pump: $100
Fbody LS1 Power Steering Pump: $150
Fbody LS1 crank pulley: $50
Fbody LS1 Tensioner: $50
PCM tuning (If you're running a 5.3L on a 0411 PCM, you need it): $400 - Still needed with an LS1
That's $550 that's still needed for an LS1 and 400 that is not needed to be spent at all (that's a 4-5 hour job to modify the harness, or just use it as is, it's fine). I'd also argue that any junkyard pull is going to have a starter with it, but even then, it's 25-30 bucks, so whatever on that I guess.
I generally see an LS1 pullout for ~2500 dollar range. That puts a 5.3L about a grand cheaper than LS1, which is about what I see when I build these cars. Whether or not a grand is worth it is up to you.