Without beating around the bush, these are the basic factors that are affecting your plants.
Started in small cups that are much too small.
Clear cups are no good, roots need complete darkness for proper growth.
Left in small cups too long, stunting growth.
Transplanted into pots that are way too small.
Photoperiod plants need 20 litre/5 gallon pots at a minimum for proper growth.
Hope this helps,.......
Organoman.