Flavor – Lessen the acidity of fruit shrub syrup

Getting the Vanilla from the bean to the taste bud takes time. While many will advocate the use of fresh vanilla beans (as you have tried), I have always preferred the flavor that is granted from a good vanilla extract. In my opinion it is stronger and better distributed throughout the dish. Whether you buy or make your own extract I think you will get a more consistent and rich flavor that way.

(note: thanks to @rfusca for providing the extract link in a previous question)

I haven't cooked chocolate with regular wine per se, but my instinct is that to get the right marriage of flavour you really might need to consider alternative approaches with both a higher sugar and alcohol content: dark chocolate is a very powerful flavour that will obliterate most wine.

So I would try using something else wine-related but with a considerable higher sugar and alcohol content: Port and chocolate certainly can complement each other well - I would recommend a tawny port (I have used this combination as a sauce for a savoury dish). You might try sherry too, but this is slightly riskier territory in my opinion.

A further alternative depending on the dish you are cooking would be to pursue your current course add a third component that will help with the overall flavour structure, typically something bittersweet and with fruit, such as redcurrant jelly.