With the permissble uncertainty I would go for interrupt based coding myself, use one interrupt to service one timer, one to service the other. Phase is the difference in timing from one interupt on one pin to the other interrupt. You can start and stop timers with external pins too. There must be a neat solution brewing now.

Most of the project is designing the timer configuration. Coding is just involved in sequencing it and reading out the timers periodically.

Steve