On how many pins? plenty of timers and ccr's on a F5529 to get 3+ running at the same time on 8+ different pins. Add the -1 to ccr0, should help with a uS drift. ms delays should not happen unless you are using other large ISR that is hogging the system. Use a 32K crystal, div TA0 by 8, you now get 0.244ms resolution and you get the whole range you need in a 16bit CCR.
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