Depending on where you have to shake it, there's the possibility the problem is in a connector rather than the harness. One common trouble spot is the big connector on the firewall, if yours is early enough to have that. I'm not sure when they dropped it and went to a harness that goes straight through to the ECU. You might try cleaning up all the connectors you can find first, and see if that helps. I imagine a whole new wiring harness would be hard to find, though a used one might be workable. If you have the earlier version, the whole engine harness should be easy to get hold of, because it plugs into that connector. The later version is two pieces, one for the injection and one for other components, and might not be so easy to replace as a whole, but you might be able to try just the injection part first.
If connectors don't help, it might be worthwhile, though time consuming, to get a good ohmmeter and start tracing, especially if you can narrow down where in the harness shaking or flexing seems to have an effect. It only takes one bad splice or broken wire somewhere in the harness to goof everything up. Annoying when it happens, and hard to find, but once you find it, easy to fix.