Mesure your line length by putting them together, not on the kite.
You can put a nail on a tree or something on the ground and just hook them all on it.
Then do what jwest said, trim powered all the way, then adjust the back lines with the knots hidden under the sleeves until your bar is all the way to the chicken loop.
As far as the safety system goes, like other said, every brand can have its little flaws.
5 lines systems can wrap around the kite, 1 line system can be problematic if you are doing a self rescue because one of your line broke, but what if the line that broke is the line that you're supposed to flag the kite with?
I personally don't have any problem with it the F-One system, BUT in the situation you're referring to, you just have to work a little your way around it.
If the kite ends up on the position you described after pulling your QR and the bar is all the way to the yellow stopper ball, just grab your safety leash (now the only thing still connecting you to the kite), start pulling on it and going back to your bar (just a few feet, don't need to go all the way to the bar) then let it go. I usually prefere doing that rather than swimming toward the kite (I know, I'm too lazy to swim). Usually, just by letting those few feet of line go will flip the kite on its back.
Unless of course you are in waist deep water and standing up in which case you are "anchoring" yourself. In that case just walk towards the kite.
As far as the QR itself, am I the only one to think that velcro is AWESOME because it's "sandfree" and doesn't need maintenance???
Let me know how it goes.