Ship models may be painted as desired as long as the alterations are not offensive and do not adversely affect another player’s experience.
Is it adversely affecting your experience?
Personaly I find the "adversely affect another player’s experience" part a bit silly (the rule that is, not you kraedin). Since that is a subjective thing that only the "other player" can realy know the truth of, it basicly means you can not repaint your models at all since it could theoraticaly "adversely affect another player’s experience".
If we ignore that part though, I'd sya paint your models how ever you want. As long as the base plates and cards are in order it should not be a problem keeping track of what ship is what. At least not more so the keeping track of which tie in a swarm is Howlrunner...
Edited by Smuggler