How do you turn off AFM on a 5.3 and what is required if the lifters are also removed?

Tune-only vs pulling the AFM hardware are different jobs.

Hardware delete (removing the AFM lifters) — Jeff Smith's list:

• Heads off: LS lifters can't be changed without removing the cylinder heads.
• Non-AFM lifters: 16 of them. AFM lifters keep moving with the cam but stop moving the pushrod when oil pressure is applied.
• Lifter valley cover: the AFM valley cover (the valve lifter oil manifold, VLOM) uses solenoids to send oil to those lifters. Replace it with a standard LS3-style cover.
• Plug the oil feeds: tap the valley stands that fed the AFM lifters and install small pipe plugs. It can be done in the car if you keep aluminum chips out of the oil; engine out is better.
• Cam: AFM engines use a different cam, so a delete is usually paired with a non-AFM cam, plus pushrods and better valve springs to match.
• Tune: the computer must be re-flashed to turn off AFM. A professional tuner is usually cheaper and easier than buying tuning software to do it yourself.

If the engine has VVT, keep it: it adds low-end torque. Pick a cam designed for VVT; a longer-duration cam may need a VVT limiter to prevent valve-to-piston contact.

Tuning details: do I need a tune?