Solar-type stars exhibit their highest levels of magnetic activity during their early convective pre-main sequence (PMS) phase of evolution. The most powerful flares from PMS stars, super-flares (SFs), have total energies 1034-1038 erg. Among >24,000 young (t < 5Myr) X-ray stars emerged from our Chandra MYStIX/SFiNCs surveys, we identify and analyze 1,086 X-ray SFs, the largest sample ever studied. We find: 1) X-ray SFs are produced by young stars of all masses over a range of evolutionary stages from protostars to diskless stars with the occurrence rate positively correlated with stellar mass. 2) A powerlaw slope in the flare energy distributions is consistent with those of optical/X-ray flaring from older stars. 3) SFs alone may speed up the processes of gas photoevaporation in disks and planets by 10-20% assuming a linear response of disks/atmospheres to flare events. We fit plasma models to the 55 brightest X-ray SFs and compare them with published SFs from young ONC and older stars. 4) The properties of PMS SFs are independent from the presence or absence of protoplanetary disks indicating star-disk magnetic fields are not involved. 5) A new correlation of loop thickness or geometry is linked to stellar mass. 6) The slope of a long-standing relationship between the X-ray luminosity and magnetic flux of various solar-stellar magnetic elements appears steeper in PMS SFs than for solar events.