Just a quick update, the main boost converter works just fine, though i dropped the direct drive by the controllers pins because it seems lie its not possible to switch from output to input fast enough for the converter to operate nicely and the protection diodes are no shottkys.
Parts count now is 6 including passives and it reliably works down to 1V, though 0.7V has worked as well and in theory even less should be possible.
here is a video of the thing running on a single empty (sub 1V) 1.2V cell. Between flashes the power consumption is just the 4uA of the watchdog and while the led is on the 25uF cap is recharged to 3.6V.
Still looking for a solution for the initial startup voltage source though...