if the difference was smaller...1/8 inch say, i would go ahead and fillet and trim.  but you indicate somewhere between 1/4 to 3/8 inch.  so i would trim it back first and put a new stitch or two in if you need to.

you can use a 1/16 drill and and make new stitch holes on the end to pull it together if your 'trimming' trims into the existing stitch.

not a big deal to put a new stitch in during the process.

h

Mine too!

[img]http://i247.photobucket.com/albums/gg152/Hugh_Jar/Fair5_zpsgjk2mbq7.jpg[/img]

Ooops, here's the picture

Yep, the bottom panels are too long. Just ignore it, do all your internal filleting and glassing, then use a belt sander or whatever and sand off the protruding part and re-establish the radius. When you round over the vertical edge for glassing, you will never know that the bottom was once a little longer. All the exposed plies will mask any sliver of fillet goo that gets exposed.   

the only point i would make about why i would cut the bottom first... to line up with the top panel.... is that at the ends, if your ends don't align, you will develop a misalignment on the sides of the panels....and then you could end up sanding through the veneer when you try to sand the panels flush with one another.  and also, as nemochad states...you will have a sliver of fillet...that wont match the top panels.  while all of these are minor....

25 seconds with a sharp saw and you have perfection.  why wait?

I'm in the process of stitchin the hull to the side panel now.  The front side panel & bottom lines up at the front but when I looked at the rear, the bottom extends about 3/4" longer than the side panels!

Did I do something wrong? Is this a typical issue?  Should I cut the bottom, sand and stitch it now so that it lines up with the rear side panels.  Or is there another way without cutting the bottom to line up with the side panel?