You can use a timer interrupt, calibrated to generate one interrupt each
one millisecond (this is your granularity, or resolution, isn't?).

You need to specify 3 x 16 bits reload counters, each one would contain
exactly half the value from each one of the 3 frequencies (double
frequency), necessary to flip the output pin twice per complete
frequency cycle. Then, the reload counters are loaded into 3 decrement
counters (16 bits each).

Each loop through the interrupt routine will decrement each one of the
decrement counters, when any reaches zero its correspondent port pin
output should flip level, then this decrement counter is load with its
correspondent reload counter value.

If your instrument only job is generate those 3 frequencies, *and
nothing else*, this can be done with a one millisecond timer routine,
but in this case you should have the same number of instruction cycles
executed with or without the "flip output and reload timers" steps, so
the routine would run steady without any jitter.

Remember that in all cirscunstances involving software, you will never
have the 3 wave forms happening at exactly the same time, if your
specify the same frequency for all of them. They will always have some
microseconds between edges.

Boa sorte e depois nos diga como resolveu... :)

Wagner.