My problem with MTOs is that I think "pfft, $350 deposit? That's nothing," and end up with 2-3 orders out at the same time. Then it comes time to pay the remaining balance all at once, and it hurts. And of course you keep buying shoes while your first MTOs are being made, so you never really get a break.
Just FYI: Carmina doesn't allow modifying existing designs for its MTO sales. The Greeley boot was just invented a few months back, largely in conjunction with a design from Epaulet, but there's basically no chance that they'll let you chop off a few inches from the top, and change up the lacing mechanisms.