Your primary issues will be generating specific frequencies above probably about 400KHz. Due to the 16MHz clock, your increments happen in 1/16 of 1us for your half period. This means that your period adjustments will involve integer increments of 1/16 of a microsecond. This is usually perfectly fine for <100kHz, but as you get above 100kHz, your possible increments start happening at 1-2kHz, and then get larger. This might be acceptable, but if you want 401kHz and then 402kHz, you may not be able to get it, but you'll probably be able to test at around 400kHz and at around 500kHz, but it could be off by a fair bit from your 'nominal' frequency.
A way to get around this is to find a digital or analog controlled oscillator and use that to generate your pulses. If its I2C and has multiple addresses, then your process becomes fairly simple, since you just need to control the however many different generators. After that its just I2C commands and a digital amplifier to get to whatever is an appropriate voltage.