No problems at all, i think whatever feels comfortable is acceptable. I couldnt tell you the best key to use (in my opinion of course) without seeing more of your game.
Generally though it would depend on what my character could do. In a simple mario game i would use "S" for jump and "D" as the alternate fire (as to keep both hands involved).
In a game like ghouls and ghosts (where your player has to tap a button relentlessly to hold back waves of enemies) then i would use the up arrow for jump and "D" for attack (my left is already doing enough work).
Re: the GUI - Good points i agree, as it is right now youve done a pretty good job. Interested to see how you refine it though. Keep up the good work.
Sorry for the longwinded answer. - Now back to work on mine! :)