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Nothing wrong with running a LR4 in a S-chassis. If you can get one cheaper then a 5.3L go for it. You can mod the hell out of that motor if you want more power if the block is in good shape or bore the block out to LS1 specs should if ever blow and have more room to do anything from LS1 to 383 stroker etc. The amount of aftermarket support for these motors is ridiculous.
Truck manifolds do very tall and will probably cause some hood problems. But you can pick up an LS1 manifold very cheap or an LS6 if you ever plan to go bigger for a few hundred.
As far as harnesses go, I would personally look into picking up a stand alone LS swap harness that will control the motor only. These type of harnesses only require switched 12V, ground, and fuel pump wiring. This way you can completely bypass/remove the entire clusterfuck of nissan relays under the hood that are not needed to run the LS. A remanufactured 411 pcm and frost tune for the stock 4.8L will have you up and running for $300 bucks. Add $500 for the harness and you can have the motor running in a single day. The 411 PCM will control any cable driven gen 1 LS based motor
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