Looking at your spreadsheet, I dont think the results are all that bad.
How accurate do you want the pulses to be?
If I wanted an accurate frequency, I dont think I would use a PIC but probably a divider from a crystal. But it is late, I am tired and I would have to think a bit more about that!
The scope is at very best only 2% accurate, look at the specifications in the handbook.
You have a couple of rogue values at U18 and U35 in the spreadsheet, but otherwise it is comparable to the ME frequency meter.
I have a DMM with a frequency range, the handbook says 0.2% accuracy. I dont use it to measure frequency as I have a real frequency counter which is far better.
There could be something strange happening with the pic as there is a cyclic variation through the frequency range, which I dont think is due to measurement error.
JimB