After a hair tearing out session I was finally able get all of the low level lighting patterns on to one large ATtiny2313 chip (17 outputs)
Here is my lighting plan (according to my current voltage, I can put up to 2 LEDs on one LED output)...
Landing Bays
2 rows of Landing lights in each bay will be made from fiber optics connected to 9 LEDs
both Landing Bays will be lit with warm white light, with an optional red lighting for Battlestations.
Engines
Each main engine outlet (3 main engine outlets) will have up to 2 steady white LEDs and 2 flickering low power blue LEDs
Cruise engine (1 small engine outlet) will have 1 steady red LED and 1 (or perhaps 2) flickering yellow or orange low power LEDs
Windows
All windows should be able to be lit from fiber optics connected to 1 large warm white LED
Battle Damage effect
each area of battle damage effect will contain 1 steady red LED and 2 or more fading in and out orange/Amber LEDs
ATtiny2313
Done 1 LED output Warm White for window light
Done 1 LED output Red for Battlestations light
Done 3 LED output for steady White engine light
Done 1 LED output for steady Red engine light
Done 1 LED output Red/Green blinking Nav light (1 sec on, 1 sec off
Done 9 LED outputs - Chaser for the Landing Bays