... the transition from "on the runway" to "35ft" must be at your first segment performance.
Incorrect, as JT has pointed out. The "getting to 35 ft" stage is considered part of the takeoff - where the gear is still down. The TODR from your performance calculations includes the distance where you are airborne and staggering up to 35 ft.
First segment starts from 35 ft. Second segment starts from when configuration change (e.g. gear retraction) is complete.