Trim the top, as you suggested, or route out the recessed portion as needed.
A few tips on jib unfurling and furling...
Before pulling the jib sheets to unfurl the jib, wrap them around the jib 3 or 4 times. This will load a little extra line onto the furler to ensure that the jib will roll up completely and not leave a little standing proud.
When you are ready to furl the jib, point the boat downwind and give the boat some time to maximize speed. Much easier than doing it going upwind. Keep some tension on the jib sheet while you are pulling on the furling line so that it will wrap nice and tight.