Manna Progression...

Is hamstring flexibility/pike compression the limiting factor when one can't seem to raise the legs very high? Strength in the hip flexors/quads? I foresee a very long journey with even the beginning elements on this one, while I'm progressing pretty well on other elements.

Also are these limiting factors similar to ones that might get in the way of progressing with a press handstand (i.e. the ability to fold over at the waist)?

They are both a limiting factor:

-if you have high tension in the hamstring your hips flexor must be extremely strong;

-less hamastring tension means less strenght necessary to lift the legs from the anterior chain.

Both of them are necessary to progress through manna and press to handstand variation.