Been absent for a few days. Looks like you have it handled, though.
Yes- if you were planning on minimal work and dropping in the LQ4 as-is, then you'd have problems. Since you're taking it apart, it's no big deal. Get a 58x reluctor wheel or swap the one from your 5.3 if you're taking it apart. The wheel has to be pressed onto the crankshaft, which means the crankshaft will be removed from the block. Swap your 5.3 front cover to the LQ4 or get another for a Gen4. You can leave the Gen3 cam sensor in place or (preferably) remove it and plug off the hole to ensure no leaks. You can drill and tap the block for the Gen4 knock sensors, but be careful. The holes are blind and you do not wanna drill all the way through. Copy the Gen4 location and depth exactly. There are 4x cam gears to bolt to Gen3 cams (Gen3 has three bolts, Gen4 uses one large bolt), GM part no. 12586481. This is a common part since most aftermarket LS cams are made for the Gen3 three-bolt pattern. Also, IIRC, you might have to swap two wires around on the cam sensor. I think the circuits are "polarized" opposite between the two gens of engines. Swap your intake manifold onto the LQ4 and your factory harness will be plug-and-play.