If you have sewn along the edges of the apron, which is a trapezoid shape wider at the bottom, then if you try to line up the horizontals of the cloth at any distance from the crease it will fight against it.

Personally, I leave about the right amount of cloth for the apron and the under apron pleat and then make the back pleats and waistline. I can then try on the kilt to see if it needs any shaping at the sides to make an even back hemline. For me, this can mean cutting the tops off the pleats which make up 1/4 or 1/3rd of the pleated part on each side of the centre back.

The thickness of the cloth, its maleability etc all affect how it makes a three dimensional surface over a rather irregular solid shape, and the large pleats at the edge of the apron provide an ideal point at which to insert a twist which alters the height of the waistline either at the front or the back to give a correct fit.

I leave the edges of the apron and under apron free, and use safety pins to hold the large pleats so they can be adjusted so the apron flares and the pleats do not buckle or twist in wear. This might take several days of wearing the part finished kilt, adjusting the safety pins until the upper edge and fell can be sewn.