My comments are based on your statement that it was running but ROUGH...if it was actually running, that's got nothing to do with VATS.

Was your starter enable relay jumped? did someone jump the wrong wires and cause a short? They don't just melt. If the relay is actually distorted physically and melted, it was shorted BUT the short has to be in the yellow wires that are the HOT wires...
If its only the black goo you see on the plug..thats GM grease used to seal off electrical components. You should see the headlite actuator relays...

I'm not going to guess and you are not open to whats been presented, so I will leave you with this...

the starter enable relay will not stop the inj pulse. THAT comes from the vats module, which looks for the key resistance to complete the circuit.
go find the key value and get a resistor the same value and install it in the cable in the column. Measure the key pellet.

If the module is functional that is a temp bypass that will allow the module to operate the inj.
If the inj still do not cycle, the module may be at fault. The bypass module is available UPS ground. If you want to locate your own, search google and good luck. They get expensive.

Do you KNOW that you have fuel pressure? and good ignition? When starting, the ECM controls the fuel pump and will NOT allow the pump to run UNTIL the engine turns over @ a min 300 rpm without ANY starter voltage. This signal originates from the dist that tells the ECM the engine is running so the ECM then enables the fuel pump to run and maintain tension on the rails. It is designed this way to prevent flooding. The system can still flood when ANY single inj shorts out and causes the entire BANK to short, sticking wide open and dumping raw fuel into 4 cylinders...it runs real rough...

You claimed earlier that it ran and you found fuel inj that were bad and one that was dead. The ONLY way you could do that is IF the VATS was functional. If your noid lite shows ANY inj cycling then the vats module is OK.
Again, if you just WANT to have a vats problem, you can bypass it and sleep easy. Otherwise, if it runs, if the noid lite does anything, the problem is NOT with VATS.

Your FSM should help confirm what I've attempted to explain to you here.
good luck.

 

I hope You understand that I agree with what you are saying. There were several issues that I was sorting regarding this 88. no cranking, 1/4 tank of bad Fuel, a disconnected fuel pump ground, and a bad starter relay. As these initial things were being sorted headway was made. I regained fuel pressure, and the car began to crank. Then on one attempted I was able to get the car started with starter fluid then it did not start again that day and I was not getting pulse. I was however able to scan for codes and got 46. I then disconnected the battery, which reset the ecu apparently and I was able to start the car barely. On doing research from past post, I decided to remove Vats only because of the injectors not firing each time I got code 46. I have since tied of the starter relay behind the dash and have ordered a bypass unit to send the signal to the ecu for injector pulse. Once that is complete I will then swap out the injectors and do a full tune up which includes timing, spark plugs coil cap rotor fuel filter, ignition module etc etc. Im doing this so I know at least the baseline that Im starting from will be with fresh key components and without the potential of vats ever being the issue. As I look at the other symptoms that the car is giving such as glowing cats: Yes you are correct there are other issues at play. For this reason when I swap out the injectors I will also swap out the FPR and TPS just so I know they are fresh. Since the car was sitting for so long Maybe the cats were clogged as well who knows. But tonight for instance the car started up faster then in the past with a bad idle who knows why maybe the fresh gas and injector cleaner...maybe the remaining vats system worked this time who knows.....But I have to say working on this car has been an amazing experience and I do value the information and cautions Ive received from this forum. Nothing is taken personal and nothing is meant to be personal. No worries I will be asking more questions in the future .....for instance what is this sensor that is on this foil wrapped tube that is just above the valve cover...its white and has a wire coming from it? its extremely loose.

 

Condescending much? For Christs sakes the kids pulling a code 46, and you act like he's screwed up for contemplating it. God you're not my friend!
Good information in a supportive tone is one thing, but to chastise to make up for lack of self esteem is quite another issue. Let's hope you don't have a dog.

http://www.chevythunder.com/code_46_vats.htm

 

That is the EGR temperature switch. It tells the ECM that the EGR system is working. If it doesn't you'll get an error code 32.

The ECM commands EGR by turning on the EGR solenoid mounted on the thermostat housing. The EGR solenoid applies vacuum to the EGR valve. When the EGR valve opens, hot exhaust gasses travel through that tube and into the intake manifold. From there they go into the plenum. When the EGR temperature switch senses the hot exhaust gasses going through the EGR tube it sends a ground signal to the ECM to tell it that the EGR system is working.

It's quite common for the ceramic part of the switch to break. Sometimes the wire breaks off at the top because it make a sharp bend there.

 

After installing the vats bypass unit to send a 30hz signal to the ECU. Checked the injectors and they all pulsed and had ohm reading of 17.9 to 17.5. The car starts up with no issues and without the need of starter fluid. She ran very smoothly So thank all for your help on this matter. Its clear though that I need to do an upper engine rebuild due to antifreeze in my oil. I will do a head gasket replacement as well as a valve job on the heads. Will keep you updated once its complete.
Thanks again.