Lots more information needed. Start with what processor is in it and the actual code, and what you mean by
cheeseclock:
I need the ability to turn some of the remaining digital outputs on and off based on time since I can't use the pwm output to do what I'd like it to do.
as you suggest you want a software-based PWM (so high frequency switching) rather than just switching something on or off for seconds or longer at a time.