I need some big help

Hi everyone, I am new to the site and am loving it so far. I am hoping someone can give me advice on my van. It is a 1989 Chev Astro 4.3 L. The 8th digit is a Z. My Y pipe for the exhaust split recently so I went to the junkyard where I knew a friend of mine took his van there, his van ran good so I took the y pipe from it and replaced it with mine. My wife took the van to the grocery store and ran out of gas along the way. I drove down in my other vehicle and put new gas in a gas can and placed it in the tank and drove it home. I shut the van off and left it until the next day and I went to drive it, that's when I noticed it, when I accelerate it sputters and then hesitates and then goes normal, but sometimes it will backfire up thru the TBI unit and knock the air cleaner lid off to the side, almost all the time when I am in drive at idle (waiting for a light to turn green) the engine will change idle speeds all the time, not by much but enough to notice.
This is what I have done so far to try and locate the problem, I took the EGR valve off and looked for carbon build up, I never noticed a big chunk but I cleaned it up the best I could, I took each spark plug wire off the distributor one at a time and each one made the engine act different. I took off the rotor and cleaned it up and looked for moisture and found none. I changed the fuel filter and then took the van for a test drive and it still blew the air claner lid off to the side.
If there is something out there that can help me with this it is very appreciated. Thank you very much. Chris.

Welcome to the forum! We'll do our best to help you with your problem.

I doubt if running out of fuel has anything to do with the problems you are encountering now, so we'll start with the basics.

Does the check engine light come on with the key on, and the engine off? Does the check engine light come on with the engine running? If so, what codes are stored? How many miles since the last tune up? What was replaced at the last tune up? What is the fuel pressure?

Fluctuating idle speed accompanied with induction, (backfire through the intake) could easily be a vacuum leak causing a lean condition.

Faults with secondary ignition parts such as a faulty distributor cap, rotor, ignition wires, spark plugs and ignition coil can also cause induction while the engine is under a load, yet run normally at idle. In many cases, faults with these items are not visible or easily diagnosed without proper test equipment. Unfortunately that leaves trial and error, the process of elimination, and the SWAG method, (scientific wild ass guess) the only avenues to pursue. Post the results to the above questions and we'll go from there. Hope this helps.

Old Master is right on on this one. My 89 started to back fire thru the TBI under load, especialy right after the 1-2 upshift. Turned out to be spark plug wires. Not an easy job to do, I suggest taking it to a tune up shop that has a lift and get a complete tune up.