Rather than swap whole injectors, swap adjacent injector connections, and you can then see if the problem follows the injector or the harness. Although injector firing is timed, it's not so critical and will work well enough for the test.
Assuming you've already eliminated spark problems... if an injector is firing correctly, when you pull the connector at idle, the engine will bog slightly, then recover. If the injector is not firing, you'll see no change. Do the test with connectors normal, then shut down, swap connector of whatever injector shows bad with its nearest neighbor, and try again.
Have you tested vacuum? It's a good way to narrow things down. A bad injector won't show much on vacuum, but of course mechanical problems will, and so, usually, will spark problems.
edit to add: I had similar problems with a 93 that had a bad splice in the injector harness, but that one got worse when it heated up. Still, it may be worthwile to get an ohmmeter and check for resistance in the harness wires. Look especially at the +12 volt supply to the injectors, which is sourced at the distributor, and sent to all injectors via splices (the injectors are switched by the PCM on the negative side).