I think, from the sound of the result, that you made the same mistake in thinking that I did early on about what the canvas is actually for.

The mistake in thinking is that you solidly anchor the canvas and pleats together. that somehow the strength comes from the combination of the two. This is incorrect.
And this will create puckers like what you describe.

The concept is to loosely baste the canvas to the inside of the kilt. This sort of keeps things from bunching up. but the canvas and the pleats should both move independently from each other. The canvas just supports the pleats.

When you wear the kilt you are actually wearing the canvas. The pleats float loosely over the canvas with no stress on the stitching.

When stitching the canvas think basting. the stitches should be big, loose and go just through the inside of the pleats not all the way to the outside.