Hello Sam,
I think the best option you have is to use the High-resolution/wake up timer. The High-Resolution/Wake-up timer is a 16-bit down counter which is clocked at a 1kHz rate when it's enabled. I recommend you checking chapter 18 of the user manual.


Regarding your options that might please see my comments below.
1.- Leave FRO on in deep sleep. You are correct, all the timers that you mentioned are forced off when you enter into deep-sleep mode.
2.- CLKOUT Pin wired to a pin interrupt. The problem with this option is that the MCU will wake up each time it detects the pin interrupt, you cannot configure the MCU to wake up until the fourth time that the pin interrupts occur.
3.- Achieve <200uA current draw without deep sleep. First I would recommend you to try the option I mentioned before. Waking up the MCU with the High-Resolution/wake-up timer.
Hope it helps!
Victor.
-----------------------------------------------------------------------------------------------------------------------
Note: If this post answers your question, please click the Correct Answer button. Thank you!
-----------------------------------------------------------------------------------------------------------------------