For indoors, 2 gallons is small and 5 is big. Also, why would you get a 5 gallon pot and only fill it with 3 gallons of soil? If your plants are only going to go 3 months from start to finish, you don't need more than 3 gallons. You'll save space using 3 instead of 5 gallons with 3 gallons of soil.
Like mentioned above, focus on your roots....big strong roots down there will give you bigger results up there. Your problem is also your nutes...if you're using nothing but fox farms 3 pack, that's not enough. Also, a single 1000 in a 9 x 9 room is pretty weak...Your plants will grow as good as your most limiting factor. If you're worried about electricity consumption and that sort of stuff, look into trading your single 1000 with (2) 600's. You'll get 1,200 watts in that room using just about the same ampage plus you'll have 2 light point sources. Not to mention all of your lights will be a lot closer to the light source.
One thing you could do with the different size plants, is put the small ones in the middle and surround them with the taller ones. Just rotate the taller ones a quarter turn every few days.....
Hope this helps and good luck