Ok since no one really responded to your questions directly and just dictated what should be done instead I will.

The flies - Well from my experience after just transplanting into some (non fox farms) organic soil. yeah yeah I'm cheap I know. The organic stuff seems to attract them. I never had that problem with my Premium perlite potting mix. (W/E it was). But now I do.

Nutes - Don't use them yet, wait until they develop at least 4-5 nodes ( pair of branches) Then it'll be safe to use them on your lil babies.

CFL - The CFL is fine for seeding. ( Did you try to germinate? most swear by the paper towel trick, I just stuck mine in a glass of water 3-4 at a time and let it sit 1-2 nights and waited for a white tail to pop out. about 80% worked but I call that good for bagseed.)

Back to the light. I'd say your fine with it, I sprouted under my kitchen sink fluor tube. It was a 12" 30 watt I believe. Took awhile but it worked, so no reason why your 26w CFL won't do better in a closed space.( Might help to also to put your CFL on it's side, I've read it uses the light more efficiently)

Fan - Don't worry about a fan right now, it'll help after they sprout, but you might have some stagnant air in the cups if the soil line is low, which with the organic could make your pest problem worse.(Where the fan might help, move stagnant air and disrupts the bugs ability to fly.)

Either way don't let people tell you, it's not possible. I know mine are now over a foot tall after just experimenting in crappy conditions and upgrading as I went along and got more serious. I'll post any more info that might help as it comes.

I look forward to your progress.

Good Luck my friend.