You're not alone on the leg issue. My legs are the same length, but one knee is higher than the other by about 5/8 inch. It doesn't sound like much but it can be crazy making!! I had a similar struggle as you with kilt length and a full length mirror, "up a little more too short on the left...down a little more sh*# too long on the right!!" It took a bit of fiddling with it and then one post construction alteration ( a big job for the kilt maker of shortening the rise, lengthening the pleats) to get the length right. I still dink around with my kilt hose every time I put them on because the same issue occurs with them, only on the bottom of my knees!! Ohhhhh, the trials and tribulations of the kilted life

My suggestion on the kilt fit would be to do what you are doing, use the kilt you have to decide where you would like the new kilt to sit. Basic guidelines for traditional kilts are at or above the navel, rarely below that. And for length, an inch or so above the knee to mid knee, never below that. Of course, there are no kilt police, but those are the conventional points to wear a kilt.

Tell your kilt maker where you would like the kilt to sit, as learned from your experimenting, and they will tell you how to take the measurements based on their style.

Not a bad problem to have really

Good luck!