Your comments made me go back and read through books one and two.I think it's important to clarify that the starter cranking does not rule out a VATS issue.
In the pass key section the trouble shooting chart #2 is titled: "Engine Cranks But Won't Start"
In the DTC 46 it says starts and stalls in 1.7 seconds. But there is no test chart for "Starts But Stalls in 1.7 seconds"
What I got out of it all is that a VATS module does not always trigger the theft deterrent relay and that can be normal operation. If the PWM does not make it to the PCM it may sound like the engine started (1.7sec).
More importantly is does not seem possible to easily diagnose a VATS problem with out a code reader and a multi meter that will respond in some way to the PWM.
A cheap digital meter might just read blank or "OL" or change ranges where a analog or better digital meter would show voltage(and/or hertz). As usual a oscilloscope would be handy.
Other than the key resistor input all the VATS circuits ground other components. So a bad ground might allow the VATS to seem to function but not have enough conductivity to ground the relay or send the correct PWM to the PCM.This may be a long shot,but look closely at the grounds bolted to the icm/ignition coil mounting stud at front driver cyl head.The VATS grounds there.These eyelet grounds are notorious for corroding and or breaking off the eyelet lug,if never attended to.
On old cars I add ground cables. In this case I add one to the ICM bolt to the battery ground wire.(at the fender lead or block lead)
It is amazing how much better the charging system on some cars operate when you add a ground wire from the alternator case to a negative battery lead wire. Factory alternator to block electrical connections are not always perfect after 25 years.