Bad gas (gasoline) problem

[DZEE'S LX]

I'm helping a friend with an 89 5.0 EFI Cougar that I think has stale gas. I'm posting here because I have always gotten great info from you all on this site and I believe the components of the system are all but the same as the Stangs

The car had been sitting for 2-3 yrs before he bought it. It was running when it was last parked by the previuos owner.
The tank was nearly empty and he put a few gallons of fresh gas in the tank.
It will turn over fine with the starter but won't fire or even sputter. I used a timing light and it has spark. The fuel pump runs for the normal second or two and then shuts off - so I think it has fuel pressure.
I'm thinking all the lines and filter have old gas/varnish or water in them. Since the engine wont fire I don't know if the old junk will push through so the new gas can make it to the injectors.

What is the best way to flush all this out of the tank and fuel system? A new fuel filter is a given, but it would be nice to get this thing running without having to tow it to a shop.

Thanks