I've been trying to picture in my head the part you are talking about, if I'm right you should understand what I'm about to say .....
Remove approx 6inches of gutter either by a grinder or hacksaw, then with a pointed hammer (like the bottom one in the picture)
Beat both edges about 3/8 to 1/2 inch below the bodyline, then fill with weld making sure you get good penatration without too much heat, when you have done this section MISS out 6 inches (to retain shape and strength) start all over repeating untill you have done all the sections that you can't to the rear of, then go back and do the bits you left in for strength.
I hope this helps.
Rob.