RTM_TimerCalc V1.01 is here. Get your copy at the Download Section of this site
With this Desktop application, you can generate correct Arduino PWM and Interrupt source code!
Description of capabilities here.
See the Video Demonstration on YouTube
Dial up the exact waveforms you want. Specify Interrupts down to the millisecond.
Its free to use. Go to the Download section of this site and grab your copy.