Your kiln is not working right. It is supposed to fire reasonably evenly, and a cone difference between the middle shelf and the top and bottom is too much of a difference. It is not a matter of stacking the shelves differently. You have tried that, and it hasn't helped. It is not a matter of needing to make extensive modifications to your kiln, which would void your warranty. It is a new kiln, so wear isn't a factor. I would call Skutt again and tell the tech that you've tried leaving out various peeps and you're still having trouble with the evenness of the firings. I have a 3-year old 1027 that I fire regularly, and over time I've started having some trouble with the evenness of the firings top to bottom. Some parts might be starting to wear on my kiln. But when it was new, it fired evenly enough that I never had a problem with the glazes maturing at the top or bottom when the middle shelf's cone read a good cone 6 firing, and even now I can put the bottom shelf up a few inches and stop loading a little before the top and get pretty good glaze maturity throughout the kiln. It sounds like your kiln is firing so unevenly that you can't really use anything but the middle of the kiln, and that's not how the kiln is supposed to work. Skutt should fix it under warranty.