I am getting the codes using my Superchips Flashpaq tuner. I still get the SES lite, though no 1316 code. Drove it and still get the shudder/vibration.
If it's related to disconnecting the battery, why after removing codes do they come back even though battery hasn't been disconnected again?
OK first, that Superchips thing isn't what you need to really diagnose your problem (especially an IDM issue) find someone with a Real scanner if you want to know what codes you have....
Here's what those two codes are all about;
P0603-KAM Memory Loss (KAM = KeepAliveMemory, basically RAM that's been cleared by the power loss.)
P1000-OBD II Monitor Checks Incomplete, More Driving Required. (I've never seen this on my truck, I think it's what Superchips mis-applies to your diesel. It's basically saying the "drive" parameters have not yet been met to check the PCM for emissions (at least that's what I've seen on gas vehicles)).
BOTH those codes will go away on their own after awhile. I don't believe either will set the SES light ON though.
Again, hard to do real diagnosis without real tools. Find someone with the right scanner (Auto Parts stores don't have them, you need to find somewhere that does...)