So I ran a program overnight to compute my true CPU frequency based on the RTC clock.
I used the brute force approach, because I didn't want to deal with signal processing of both clocks so I averaged 8 hours worth of it.
Otherwise I will have to sample the RTC with respect the QPC and viceversa and with some math get the number, but it was late so brute force it is.
So the speed of the CPU's performance counter according to the RTC is 2399913708.04589784 Hz.
Note the decimal part is because we are dealing with two signals of different periods, so that is the frequency taking away the time discreet offset of the RTC.
Having that calibration data I can preload the average of 8 hours worth of data and run my program.
With that frequency value I have a 1ns precise clock (based on the average second of the RTC over 8 hours)
The first value is the second variaton of the RTC with respect of the performance counter per second.
The second value is the average mean time according to the performance counter. (pretty much absorbing the waveform from the RTC being sampled at random discreet points.
Frequency MHz = 2399.913708
second drift = -0.000006850, average drift/s = -0.000000000
second drift = 0.000006455, average drift/s = -0.000000000
second drift = -0.000000276, average drift/s = -0.000000000
second drift = 0.000000286, average drift/s = -0.000000000
second drift = 0.000000043, average drift/s = -0.000000000
second drift = 0.000000991, average drift/s = 0.000000000
second drift = -0.000000261, average drift/s = 0.000000000
second drift = -0.000006809, average drift/s = -0.000000000
second drift = 0.000006549, average drift/s = 0.000000000
second drift = 0.000000834, average drift/s = 0.000000000
second drift = -0.000001701, average drift/s = -0.000000000
second drift = -0.000000164, average drift/s = -0.000000000
second drift = 0.000001659, average drift/s = 0.000000000
second drift = 0.000000200, average drift/s = 0.000000000
second drift = -0.000000385, average drift/s = 0.000000000
second drift = -0.000000490, average drift/s = 0.000000000
second drift = -0.000000299, average drift/s = -0.000000000
second drift = 0.000000568, average drift/s = 0.000000000
second drift = 0.000000264, average drift/s = 0.000000000
second drift = -0.000000239, average drift/s = 0.000000000
second drift = 0.000001205, average drift/s = 0.000000000
second drift = -0.000000359, average drift/s = 0.000000000
second drift = -0.000000048, average drift/s = 0.000000000
second drift = -0.000000963, average drift/s = 0.000000000
second drift = 0.000002439, average drift/s = 0.000000000
second drift = -0.000000310, average drift/s = 0.000000000
second drift = -0.000000569, average drift/s = 0.000000000
second drift = -0.000000340, average drift/s = 0.000000000
second drift = -0.000006100, average drift/s = -0.000000000
second drift = 0.000006703, average drift/s = 0.000000000
second drift = 0.000000200, average drift/s = 0.000000000
second drift = 0.000000946, average drift/s = 0.000000000
second drift = -0.000001308, average drift/s = 0.000000000
second drift = 0.000000774, average drift/s = 0.000000000
second drift = -0.000000839, average drift/s = 0.000000000
second drift = 0.000000358, average drift/s = 0.000000000
second drift = -0.000005879, average drift/s = -0.000000000
second drift = 0.000006286, average drift/s = 0.000000000
second drift = 0.000002079, average drift/s = 0.000000000
second drift = -0.000000846, average drift/s = 0.000000000
second drift = -0.000000895, average drift/s = 0.000000000
second drift = 0.000023038, average drift/s = 0.000000000
second drift = -0.000022031, average drift/s = 0.000000000
second drift = -0.000000205, average drift/s = 0.000000000
second drift = -0.000000003, average drift/s = 0.000000000
second drift = 0.000000440, average drift/s = 0.000000000
second drift = -0.000001143, average drift/s = 0.000000000
second drift = 0.000001111, average drift/s = 0.000000000
second drift = 0.000000564, average drift/s = 0.000000000
second drift = -0.000001690, average drift/s = 0.000000000
second drift = 0.000000616, average drift/s = 0.000000000
second drift = 0.000000440, average drift/s = 0.000000000
second drift = -0.000000145, average drift/s = 0.000000000
second drift = 0.000000530, average drift/s = 0.000000000
second drift = -0.000000636, average drift/s = 0.000000000
second drift = 0.000001153, average drift/s = 0.000000000
second drift = -0.000001064, average drift/s = 0.000000000
second drift = 0.000000575, average drift/s = 0.000000000
second drift = 0.000000628, average drift/s = 0.000000000
second drift = -0.000000483, average drift/s = 0.000000000
second drift = 0.000000268, average drift/s = 0.000000000
second drift = -0.000000115, average drift/s = 0.000000000
second drift = -0.000000370, average drift/s = 0.000000000
second drift = 0.000000440, average drift/s = 0.000000000
second drift = 0.000024925, average drift/s = 0.000000000
second drift = -0.000024716, average drift/s = 0.000000000
second drift = -0.000000269, average drift/s = 0.000000000
second drift = 0.000001423, average drift/s = 0.000000000
second drift = -0.000000318, average drift/s = 0.000000000
second drift = 0.000002330, average drift/s = 0.000000000
second drift = -0.000002838, average drift/s = 0.000000000
second drift = 0.000001966, average drift/s = 0.000000000
second drift = -0.000001476, average drift/s = 0.000000000
second drift = 0.000000020, average drift/s = 0.000000000
second drift = 0.000000598, average drift/s = 0.000000000
second drift = 0.000000155, average drift/s = 0.000000000
second drift = 0.000000219, average drift/s = 0.000000000
second drift = -0.000001004, average drift/s = 0.000000000
second drift = 0.000000425, average drift/s = 0.000000000
second drift = 0.000000249, average drift/s = 0.000000000
second drift = 0.000000024, average drift/s = 0.000000000
second drift = -0.000000025, average drift/s = 0.000000000
second drift = -0.000000625, average drift/s = 0.000000000
second drift = -0.000000104, average drift/s = 0.000000000
second drift = 0.000002435, average drift/s = 0.000000000
second drift = -0.000001634, average drift/s = 0.000000000
second drift = -0.000001053, average drift/s = 0.000000000
second drift = 0.000000635, average drift/s = 0.000000000
second drift = 0.000000159, average drift/s = 0.000000000
second drift = -0.000000063, average drift/s = 0.000000000
second drift = 0.000000380, average drift/s = 0.000000000
second drift = -0.000000179, average drift/s = 0.000000000
second drift = 0.000000538, average drift/s = 0.000000000
second drift = 0.000000129, average drift/s = 0.000000000
second drift = -0.000000693, average drift/s = 0.000000000
second drift = 0.000000264, average drift/s = 0.000000000
second drift = -0.000000914, average drift/s = 0.000000000
second drift = 0.000001531, average drift/s = 0.000000000
second drift = -0.000001079, average drift/s = 0.000000000
second drift = 0.000000174, average drift/s = 0.000000000
second drift = 0.000000609, average drift/s = 0.000000000
second drift = 0.000000980, average drift/s = 0.000000000
second drift = -0.000000078, average drift/s = 0.000000000
second drift = -0.000000884, average drift/s = 0.000000000
second drift = 0.000000489, average drift/s = 0.000000000
second drift = -0.000000745, average drift/s = 0.000000000
I'm going to start it again and let it run for a long time.