Making a fountain pen is no more complicated than a ballpoint, other than you will definitely have two tubes to deal with, whereas ballpoints often only have one. At the end of the day though you are still turning blanks to predetermined sizes then pressing components into the tubes. Where you do have to exercise a bit more care is in lining up the grain on both parts, as it's quite a nice touch to have the smartest part of the blanks in line with the upper side of the nib when the cap's off, when the cap's on closed, and if the cap fits on the blunt end (if the cap posts) when it's fitted "posted" too.
I know a lot of people get apprehensive when faced with their first fountain pen, and I understand why, but if you just look at it as a sort of fat slimline, then the process is just the same. And if it all goes wrong you can always part the blanks off the tubes and start again.