The reason it changes the calibrated delay is because you are now hitting that delay(the one it changed it to) via what you updated your results with. So even if you think you always hit 600, today you might be having quicker/slower reactions and thus your calibrated delay is changed. This is why calibrating is all but useless(still helpful to have a starting point in the timer) as timers will generally be able to narrow down the range you're hitting in better than you can.
^Read above explanation
Journal flips are 2 each, Walking with X amount of Pokemon in your party for 128 steps advances by that many frames, trouble is you never know where your step counter is at and missing by 1 frame would be rather unfortunate at 20,000.
Oak's Pokemon Talk, in the upper right. This one advances up to 14-18 frames, and is what you should use if you want to hit very large frames. But remember to use Elm towards the end due to the inconsistencies. And as far as I can remember switching to Hoenn Sound doesn't advance the frame, just make sure you have the right day and encounter slot calculated for your frame.
This written guide is the best place to start without cluttering up the thread with an open discussion. Read through it and if you have any questions feel free to post them here or in the 5th Generation RNG thread below this one.
Which guide are you referring to? I've read through the OP but that's not getting my anywhere, it doesn't even seem to be discussing BW2