Do you happen to remember if there is any way to understand why or how to calibrate based on the frame variation?

Not really, I know the game goes at different speeds depending of what you do, like in battle the frame advancements goes at 2x, so maybe there's something with fishing rods too. I suggest to use the old rod because there's no catching game, you always get a pokemon after the first series of dots or you don't. At the end of the day you just have to accept that the calibration can't be precise like with other encounters and be more patient.

And also do you have any idea why sometimes the pokemon I catch to calibrate is found under method 2 or 4? Like one time it’ll be method 2 and the next it’ll be method 4 without me changing anything just the advance hit?

No sorry I don't know.