If I understand correctly, you describe these various problems as sometimes present, sometimes not. You note the engine runs fine at first then drivability issues of several types appear, plus you have a changing set of fault codes that most recently included a series of PT-CAN bus communication errors involving the DME. The intermittent nature of these things is not typical for a failed turbo or a failed DME but could indicate an electric connector problem. In any case, I cannot come up with a reasonable hypothesis for how a turbo problem could result in this constellation of issues.
Since the problems occurred after driving through deep water, have you checked the DME the box for water entry? Have you removed the DME connectors and looked for corrosion?