what's your timer set to? I would have my lights on an 18 hours on, 6 hours off, cycle, and the off cycle is during the warmest part of the day. You can plant into those 20 oz dixie cups at any time, many start them in those cups. just remember to poke holes at the bottom of the cups and add some perlite to your soil mixture to aid in drainage, it really helps the plant grow faster.

Are you using only the CFLs right now? Or both? your plants don't need too much light yet because they are so young, so go easy on em. I would use the CFLs until all your plants have their secondary leaves. then you can blast em with the HPS.

You can start flowering them at any time, but I would advise let them get at least 8-12 inches tall before initiating the flowering cycle.