How do you delete VATS and set the tach signal in one PCM flash?

Here is what the documentation says. Each point links to its source; details depend on your exact computer, harness and transmission.

Tach and speedometer signals

• LS Control System kit: The 2 pulse/rev tach output may correspond to a 4-cylinder setup on some tachometers or transmission controllers. (Chevrolet Performance)
• Chevrolet Performance LS harness: The 2 pulse-per-rev tach output requires the tachometer to be set to 4-cylinder. (MotorTrend)

VATS / anti-theft

• P01, P59, E38, E67: In the factory architecture the theft decision lives outside the PCM: the IPC/BCM decoder interprets the R-Code and transmits the approval to the PCM, so a swap with no BCM must have the check disabled in the PCM itself. (Directed Electronics)
• P01, P59; LS1, LM7, LQ4, LR4, L59, LS6; 1997-2007: HP Tuners official VATS-disable procedure for Gen III PCMs (including P01/0411): in VCM Editor go to the Systems tab > Security > VATS Control and select 'None', save the file, then perform a Write Entire (not a calibration-only write). (HP Tuners)
• P01, P59; 1997-2007: VCM Suite Online Help defines the Gen III VATS Control types as: Serial = Class 2 VATS, PWM = PWM VATS, None = VATS system is non-existent or disabled; VATS Fuel Cut determines whether fuel is cut when VATS fails. (HP Tuners)
• P59; LM7; 1999-2006: MotorTrend's DIY LS swap wiring guide (based on a 2002 Tahoe 5.3 harness) separates physical harness simplification from PCM reprogramming, and says the PCM must be reprogrammed to remove VATS. (MotorTrend)

Computer and tune

• In HP Tuners VCM Editor, VATS is disabled by going to the System tab, then Security, setting VATS Control to 'None', saving the file, and performing a Write Entire. A VATS disable is required on swapped powertrains so the engine starts and runs; it is not required when tuning a stock vehicle. (HP Tuners (official channel))

Confirm against the instructions for your exact parts before wiring. More: Tach and speedometer signals in our tuning guide.