Since this happened after replacing the battery you gotta check some fuses in the engine compartment fuse box. I think you have 2 IGN fuses and 2 PCM fuses as well as a DIS fuse (for the ICM ((probably good as you're getting spark)) and 2 INJ fuses. ( you're getting power to the injectors so they're probably good too but what the heck, you have the lid off the box, check them all anyway)

AND because this happened after a battery disconnect you have to entertain maybe an issue the theft deterrent system. But that should be easy enough. I think you have GM's Pass-Key (maybe Passlock) but if the issue was with this, you'd get either a flashing dash light or in your case maybe a message in the driver information center (depending on your model).

Anyway, the '99 4.6 uses a bypass ignition system. You're getting spark so the Crankshaft Position Sensor is good as well as that part of the ICM (Ignition Control Module). (The PCM isn't involved in "spark" during startup. It takes spark control when the engine reaches 200 RPMs+)

So then, (fuses good) it's between the ICM outputting an RPM signal to the PCM, and then the PCM sending the ground signal to control the fuel injector pulse.
(That ICM can be faulty and allow the ignition bypass (spark) to be provided during start up, but still not outputting an RPM signal to the PCM to allow it to control injector pulse ((or timing)).

So, are you seeing an RPM signal (on the Tachometer if you have one) or on the scanner during Cranking?

No RPM signal from the ICM to the PCM means No injector pulse is possible.

So here, you may suspect a faulty Ignition Control Module (OR, as in all cases with everything electrical, a wiring/connector issue in the circuit)