"You should be able to start and run without the FPR hooked to the vacuum. Just plug the line. The FPR is only there for adding fuel pressure under load."

Wrong. The FPR needs vacuum to "regulate" the normal 36±psi. The vacuum drops when the throttle opens wide, raising pressure to 43±psi for acceleration. If you pull and plug the vac line, leaving the FPR port open to atmospheric pressure, it's the same as wide open throttle.

The '89 240 doesn't have a Cold Start Injector.
If you suspect it's flooding via the injectors, just unplug them.

The extra gas has probably washed the cylinder walls dry of oil. This can drastically lower the compression, making starting hard if not impossible. Add an ounce or two to each cylinder thru the plug holes, then crank it over a few revs with the 25A fuse pulled to kill the fuel and ignition.

I believe the only known (or at least common) 561 pink label ECU problem is causing a no-start by failing to energize the Fuel relay when it should.
--
Bruce Young, '93 940-NA (current), 240s (one V8), 140s, 122s, since '63.