An engine that runs well when cold but misfires when It’s warmed up is often a victim of poor air-fuel mixture. That can be caused by an air-leak (such as the intake manifold gasket you’ve already changed) a crack in any of the intake plumbing, faulty fuel injectors, a worn fuel pump, a corrupted ECU (computer), blocked fuel line or about a thousand other things.
But in this case, knowing the Ford AU Falcon’s engine, I’d be taking a close look at the ignition system, specifically the coil pack. These have been known to fail regularly, often displaying their problems including a rough idle, once the engine has warmed up; precisely the symptoms you’ve noted. That said, rather than rush out and buy a new coil pack, have the vehicle scanned electronically to rule out any other potential source for the problem.
