cranks but won't start?

Most of the internal grounds for the PCM go to the PDC. They're considered isolated or noiseless grounds. The data link connector also has one of those grounds. I think they are mainly for the digital signals going to the microprocessor for the dash and gauges and the DLC.

Do you have both connectors going to the alternator? There is also a battery temp sensor. I'm not sure whether that is absolutely necessary or not but it does deal with the function of the alternator.