One potential hitch-in-your-get-along is the number of available PWM pins. The Instructables tutorial uses three of the six 1 PWM pins for one flame. PWM is also used to brighten / dim an LED; an effect you may want for the blue LEDs.
This hitch can be overcome with software. But, potentially, the more independent dimming and flickering LEDs, the more complicated the software becomes.
From your description, I gather that you want three independent flames (eyes and mouth) and a set of LEDs (the blue ones) to brighten and dim. Correct?
I have both a full size arduino board
Which one?
1 Assuming you have a Uno or similar Arduino.