You can use a multimeter to check if the hubs are generating a signal. Basically just disconnect the harness at the hub, set meter to DC voltage and then spin the tire. If you get a reading then the hub is ok and you can start tracing the harness back from there. If the hub checks out then don't be surprised to find a bad/corroded wire a foot or more back into the harness. Happens a lot. If you find green or black colored copper wire showing then there is the issue. I think since it's a 99 the harness is 2 pieces and can be replaced from the hub to the main loom conenction up front. I know my 00 GP GT is like this as I went through the exact same thing.
But like Scotty said, if the EBCM is taking a dump then I'd start there.
