I agree the plants look fantastic. My point is though, the OP needs to correct his H2O saturation and possible drainage problems 1st and foremost and when the time is appropriate transplant to a large container. I know of NO ONE on the forum that will strive to grow tree sized pepper plants out of a 3oz Dixie cup. It is just not practical. This year after 3 years of steady progression, I am going to grow my plants in 10 and 15 gal pots.
I remember some years back, a study was done where they raised a rainbow trout in a glass tube. they provided the trout with a fresh highly oxygenated water supply at the optimum temp and conditions, a constant food supply and as a result the fish grew to the constrains of the tube.
The conclusion was, given a clean and nutritious environment a fish could be raised to adulthood with out providing the usual growing space.