You shouldn't anything magical to happen with a full frame camera. Depth of field is about a stop less than you get with a DX equivalent body and lens, but you're probably looking at your images a heck of a lot closer than you did before. The higher magnification you use to examine a given scene, the more you'll notice small changes in focus. That doesn't mean it will show up in similarly sized prints, and large prints from both formats will magnify differences in focus. I'm not sure why you're having trouble with your flashes - they work pretty much the same way they did with your D300.
My personal experience switching from a DX DSLR to an FX DSLR was that it was like returning back to the 35 SLR days in terms of lens options (which I liked), and I appreciated the greater flexibility in working with images in post-processing. I quickly stopped using my D300 for normal photography and eventually converted it to infrared, which I like quite a bit.