Sorry, I misremembered- this was the post https://forum.pjrc.com/threads/28037-Teensy-3-1-and-K20-FlexTimer-config-for-FreqMeasure but apparently I was doing frequency, not pulse width.
@mborgerson - I played with this today and came up with a not so glorious workaround. I broke up the 128KB into smaller chunks of varying sizes like 16KB, 32KB and 64KB. I created another transfer buffer in DTCM that I could memcpy size_t chunks...