Thanks everybody! The advice is much appreciated. I was lacing the liner in as well, so didn't want to use my lacing punch through 4 layers... which is how we ended up with this mess. I'll give the unlacing and re-doing the holes a shot and hopefully it won't look too goofy on the edge with one side higher than the other. Nice seat by the way Chancey! Was planning on getting around to doing my own eventually. Might want some practice on another couple projects first.
Thanks!