Currently the jEdit search dialog has no Accelerators for Find nor for Replace.
I suggest to use Alt-F and Alt-E respectively.
Currently one has to Tab a lot until Replace gets the focus.
Also the visual feedback is somewhat confusing, as the focus is indicated by a blue border whereas the Find button is still completely blue, so one thinks the Find button has the focus (see attachment)
(jEdit 4.5.2, Java 1.7.0_09, XP)