This contest http://www.picbasic.co.uk/forum/showthread.php?t=14652 contains some elements of what you are wanting to do.
I did it using PWM and here is a video of 2 of those channels. The contest requires 4 independent, variable on-the-fly (blink-rate) channels.
The timebase is 10uS so the PWM frequency 25KHz. The duty cycle of the upper trace is ramped from 0-100-0% - to give pulsating effect - at about 0.5Hz. The lower one is at 1.0Hz. The required blink rate should be continuously variable in the range of 0.5-8.0Hz on each of the 4 channels/LEDs for the contest.
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