Maybe a long shot but before I knew about water destroying the clp/ssm, my car would stall occasionally at idle and hesitate from idle. Took it to a mechanic, and he checked the battery current draw, it was amps - he traced it to the CLP being in a foot of water. I replaced the CLP and about a foot or two of harness behind the connector. Maybe check the area around the CLP in the trunk for water and buy a usb adapter with voltage meter for your cigarette lighter (they're really handy - when you turn your key to start, you can see your battery voltage at start and while it's running). If you're still hunting for the issue, maybe check the current draw (even if the CLP is good). If you have a battery charger, you can check the draw without loosing the cpu memory - just put the battery charger on the battery cables, loosen and remove the neg cable while the battery charger neg. cable is still attached, then put your ammeter between the battery cable and the battery terminal, remove the neg charger cable and measure the current draw. Reclamp the battery charger to the battery cable, remove the ammeter, reconnect the cable to the battery.
-Jerry