You can find the thread "replant those leggy stems" or something like that to find a good tutorial on how to transplant those stems deeper; rule of thumb on lights for plants, just very basically 100w/plant;
you've gotten good advice about keeping your lights close--2" is what I'd say but if you can get em an inch without burning that'd be fine too.
T5 are lauded more for veg by most people but it is possible to take grows all the way through. They run a little cooler, but their intensity is a little less than HPS; With aquarium and other specialty bulbs it is possible to tailor your lights spectrum to your plants;
Beacuse T5s are a little less intense they afford a little less penetration (see inverse sq. law of light intensity), which is why you need to keep them as close to the tops of your plant as possible.
While it is not harmful to run them on a 24/0 schedule for the early part of vegetating, most will tell you at least 4 hours of dark will be beneficial for growth (plants do their growing when lights are off, they store their photosynthetically generated energy for that purpose when the lights are on);
when you transplanted from cube to FF cup, you probably shocked your plants, hence the cessation or slowing of growth. Bad news about having to transplant again for the stem length is you'll probably shock them again. Get some rooter's mycorrhizae and apply the powder directly to the root system when you try to transplant again. Btw, most people shock their plants when they transplant, very common, but, being as gentle as possible and practicing, with some other tips and tricks, helps most of us do it with minimal shock.
As unpleasant as it may be to accept, Hyde is right about clear cups--thats not a good idea. And, your foxfarm does need amending with perlite at least for aeration.
hope this helps,
P.s: don't start over; try to get these gals through: you'd be surprised how hearty these gals are. I totally fucked one grow and decided to just do the bare minimum to complete it (12/12fs, perlite, oc+ and molasses H2O). Plants turned out smokable--not great, but better than any schwag or mid-grade (if you can find that).
be easy,
Dr.J