Help! Bonsai baby needs help!

kahnbro

i want to start off by saying thank you for thinking of helping me, but heres where it all begins, last christmas i got a little kit, the breed is 'japanese black pine' and i live in east pennsylvania just so you know. the seeds came in a little container for germination, said to poke holes in the bottom and let it soak, it said after 2 days i had to put it in the refrigerator for 60 days, the way it explains it says its not supposed to sprout yet, but it did while in the refrigerator which i thought was mad, but i rolled with it kept giving it water, and just kept waiting. this is when it gets a little sad, someone unintentionally set a milk gallon on top of it, crushing it, and me too. But i kept hope i just took it out of the refrigerator close to 60 days, i just thought it would die sitting in there. So i brought it out and it kept growing! It looks nothing like the pictures in my pamphlet, no leaves (ill attach pic) but as you'll see its browning at a lot of places so i looked up ways to revive my little homie, and ive saw a lot of things i was doing wrong, like direct sunlight which i stopped a week and some change ago. I also saw things saying if theres stuff on my pot like there is that there is most likely pests, but im searching for them and i cant find them. I was thinking, oh ill just cut off all the brown roots leaves repot it and see what happens, as i started digging a little i saw the root system is all brown basically and just goes in one line and starts branching out right at the bottom, so im at the point where i have no clue so id really appreciate someone letting me know what my be wrong, be mean i dont care, tell me how it is. Tell me what you think the survival rate is, i tried to give all the information i could think of, i water regularly and i know its not under but im not sure how to tell what is over, anyone that can help please help! Lil buddy need you