What's the correct temperature to prepare confit cod?
The official position of the USDA is that all fish must be heated to 145°F (63°C), else it is considered undercooked. In practice, most people don't do it, because fish is terribly overcooked at this temperature, and they seem to mostly live through it without ill effects. With salted fish, there is even less actual risk of foodborne illness. Still, I don't think that anybody will assume the responsibility to tell you that it is "safe" when the responsible officials say it isn't. You are taking a risk, but none of us can quantify it or tell you if it is justifiable. Food science books often recommend preparing fish at temperatures lower than 63°C, but include a disclaimer that this is against food safety guidelines. 

A lower oven temperature can definitely produce a better result for your problem, because slower, more gradual heating means that you have a lesser heat gradient within the piece of fish. This means that the thin parts will overheat less in the time the center of the thick parts reaches 40°. However, this will only alleviate the problem, not eliminate it completely, unless you go for a very low temp cooking method like sous vide. If the lower oven temperature isn't enough for you, you might try other tricks to eliminate the problem, like changing the shape (e.g. by creating rolls of fish).