I doubt that the crank is flexing. I run a three-year old Ultegra crank (probably not as good as newer 105) and can't tell you what flex even feels like.

I doubt that the money spent on Ultegra or D-A will yield significantly better performance. It'll just be a tad lighter.

Run the components until they are worn, then consider replacing them with nicer gear. For the cranks, wait 'til the chainrings are worn -- say about 25,000 miles, depending on your use and conditions.

As others have noted, wheel upgrades will give more performance boost than the other items.