without more info on your soil and 'whats in it', it will be difficult to pinpoint your cause for problems.

on an experience note-
ive always and still germ in paper and transition to soil.
i've had 75-95% success.

i recently had some pop that also didnt emerge from the soil.
the seedling may have touched something of an organic nature that was too acidic or even a small piece of trace nutrient that was too potent for the new growth to withstand. likely scenario to explain why a few didnt rise above the soil.

as to when to clone, i've had good success with that also recently.
i would say between 8 and 12 nodes, depending on how healthy your plants are.

keep your plants in veg as long as you can.
i take the lowest shoots as clones when i repot into a larger pot.
i start in 16 oz solo cups,
transistion to 1 gal pots. (take clones, when they are long enough)
when i move to flower or soon therafter,
final transition to 4 gal buckets. (take clones)

i have also taken some longer tops (tips) and rooted them as clones.

this was done to slow the plant and bush it out more before moving to flower.

also sometimes my flower room is too crowded and i am stuck waiting for something to finish, so i have to delay, but, this has presented new opportunities to clone from the top and bottom.

the added benefit here is that the plants really take off and perform even better when i do finally move them to flower and i get all those clones in the process.

hope this helps.imp: