Is my pin understanding correct on the 2N3904?
Yes, you are correct in your pinout. If you look at the DATASHEET, then you can see which pins are what. 



Luckily, you have your silkscreen showing where the 'flat' side of the transistor should be facing. Using that, and the picture from the datasheet, you can see that the top of your screenshot), you have pin 1, then 2, then 3. 

Checking this on the Datasheet, it is indeed Emitter, Base, Collector.