I think altering the kilt before your son has tried it on is not a good idea- what if you needed to do a size exchange, or guessed wrong on the length??

You don't want to sew the fell down without having him first wear it, so you know where to let the pleats spread at the hips. You really can't just sew them straight down or you end up with a cylinder. Have him wear the kilt, see where the pleats fall and pin them in place at the hips.
Same for the hem- put it on him and see where it needs to be.