#2 - you're arguing against a point neither I nor (IMO) the article are trying to make. The cause of the anomalous mass die-offs is of interest, but there's no concert it's an existential threat for the Atlantic dolphin population.
#3 - irrelevant. Unless you can tell me more about the nature of the lung disease [edit: allegedly] from oil & from the virus, I'll assume the researches can distinguish between the two. That also doesn't address the hormonal abnormalities or the other symptoms they didn't enumerate.
#4 - again, irrelevant. Same comments from #1 apply. You are arguing against a point that is not being made.
#5 - If you have some sort of disagreements with the data, or the methodology of their interpretation, then by all means be specific about it. Otherwise it's hard to see how this is on topic.
As food for thought: the article doesn't mention what the size of the population is. A thousand death dolphins could be a disaster, but it also could be a statistical anomaly. Percentage-wise, the effect could be smaller than that of 25 years ago. http://www.nmfs.noaa.gov/pr/health/mmume/midatldolphins2013.... does not mention population count, either. Looking at the linked http://www.nmfs.noaa.gov/pr/health/mmume/mid-atlantic2013.ht..., I find that there are over a 100,000 dolphins that might be affected. If the deaths are across the population, I don't think any of the populations is at risk, even if this repeats itself next year. Replacement per year should be about 2,000 to keep population at 100,000.
And lung disease happens to be associated with Morbilliviruses, too (http://en.wikipedia.org/wiki/Phocine_distemper_virus)
Also, as that URL shows, there was a Morbilliviruses epidemic going on with seals in the North Sea in 1988-1992. At the time, people claimed seals would go extinct in the Wadden Sea. Now, there are 150,000 (http://www.ecomare.nl/index.php?id=4180&L=2); the population in the Wadden sea increased from 150 in 1992 to just over 3000 in 2012 (same link). Is that a sign that all is well with the environment? I doubt it. As with this article, I read "we simply don't know" between the lines.
And that's not because I think the scientists working on this aren't good. They have to make a living and have forget their maybe' sand "it's just one theory"'s in order to make the paper. Many of the so-called softer sciences are simply too hard to make accurate predictions about. Maths? Easy. Physics? AFAIK, all electrons are created equal, but things get difficult hard as soon as you have many of them. Chemistry? Already a bit harder. Biology? Some simple models make good rough predictions, but don't expect those predictions to be even remotely right every time. Psychology? You can almost forget to make reliable predictions. Sociology? Even harder.