So what are all the different ways to get EDCs and Dilithium? I know several dailies have Dilithium, and the STFs have EDC rewards (so far I have 2), but what else can I do?
I believe the only way to get EDC's are through the STF's. I just collected my first 10 and bought a dual beam antiproton [Borg] weapon. It's best to do the STF's on Wednesdays, when the specific STF grants double the EDC's.
As you mentioned, you can get dilithium from the different dailies (Defera, satellite repair, B'Tran & strange new worlds, investigate officer reports). You also get dilithium for the Doff missions (quantity varies by success) and you get 75 dilithium for dismissing DOFF's. The hourly events also reward dilithium (Fed/KDF Mirror event, Academy events). In the Academy events, you collect particle fragments and redeem them for dilithium. In the hour that the event runs, it's possible to get over 4,000 dilithium.