Just to close out this thread... It's fixed and the problem was transaxle output speed sensor. As for the rough idle on start-up? It seems that if I turn the ignition on and let the fuel pump run until it shuts off, it starts and runs perfectly. Changed the fuel filter just in case, but it seems to be more of a fuel pressure leakdown thing. Possibly bad injector? Either way, if I just wait a few seconds after turning on the ignition before cranking it-- no problems.