Didn't have that trouble with mine.  If memory serves, there are screws into the skeg from the inside of the bottom, right?  You might try dry fitting that to see if maybe it's just that the skinny end has sprung a bit.

Otherwise, yeah, shape away if it ain't too bad a fit, so that it goes where it's supposed to.

.....Michael

Thanks Michael. I ended up just sanding the ends of the curve and got it good enough that I should be able to snug it down with the screws.