I hope I didn't come off as being rude, it's just the only way to truly guarantee a seat these days. I'm not sure how the SkyBonus upgrade certificates work.
You said you found a Y class fare for less than a B fare? Are you sure about that? Y is the highest priority economy fare, upgrade wise. If you found a Y fare for 2K, that's a pretty good deal. I'd call Delta and ask about the upgrade inventory for your flights. Are the transatlantic portions on Delta metal, or KLM? As indicated previously, you can't use certificates on codeshare/partner flights.