Rust? Shock? Overwatering? oh my.

Hello Fellow Growers!
I recently after a little research decided to start my own little green friend growing in a 6 inch pot under one 15 w fl tube and one 13 w fl work light. i planted multiple seeds, and only two remained. One clearly outgrew the other and eventually the other one died off. About once or twice a week while he was still in the smaller pot i would let him sit in my windowsill moving him periodically to keep him in the sun. I even let her(hopefully) listen to ziggy marley with my headphones.(see Picture)
More recently i felt that growth had almost halted, and i saw the need to transplant. At this time the plant was 13 days, with 8 leaf sets. I transplanted him into a 3 gallon pot but only had enough soil to fill it half way. I then added two 23 watt cfl lights to the already 28 watts. bringing me to 74 watts fl. I had fed once only in the 6 inch pot an i fed once more when i transplanted it. using about half a spoonful in a cup of water. The next day i was a little surprised to see that their was no new growth i was expecting to wake up to my first set of five pointed leaves but intsead i saw droopy no larger the a half inch leaves in a very bright green color. It is now Nov 4th and I check on my baby only to see that she has developed orange almost shiny spots, which i am starting to think is rust, slight Browning around the edges, droopy top leaves which still havent grown and have got a discoloration part of which is very dark. Pictures attached show my lil guy listenin to music before transplant, the new grow location, the last set of leaves that is refusing to grow, and the rust looking spots. Any advice, help is greatly appreciated.

Usually this is a Ph problem but others here will know better than I. good luck!

Also be sure to read the sticky in plant Probs.

It was growing just fine before. only after i transplanted it was there a problem. Once i transplanted i more then doubled the amount of light then previously, I would think it would at least grow for a little longer

Anything people? I wasnt sure exactly what overwatering would look like, but i didnt think it would stunt the growth or cause those spots. Can anyone clarify if that is indeed rust?

Im starting to think that the ph may be to high. the greenmansguide suggest mixing spoonful of epsom salt in a gallon of water. I thought salt killed plants? this is also supposed to help with sulfur deficiency

now there appears to be some lower yellow spotting. growth seems to have picked up but its still going EXTREMELY slow. This plant was growing like a weed just less then a week ago? what happened.

Well i treated the plant with the epsom salt. Growth actually has continued, but instead of shooting up like it was it seems to be concentrating on foliage growth. mabye this is because the two new lights i added were warm whites. or whatever the yellower looking ones are. mabye in a lil i'll get two of the cool whites. the spots are still there an one of the leaf tips turned a lil light brown. i think this is because i double treated with the epsom salt over a couple of days and it may have been overwatered a little in the proccess. Anyone else got any ideas how to get rid of the rust? its really annoying/ugly/embarassing to show my friends my hard work only to have it stained.