This is a great guide ;>
Pokemon eme(rald)-timer :o
I just realized that the part where you type in your frames （フレーム, or fureemu）to convert them into seconds （秒に変換, 'byou ni henkan', lit. 'convert to seconds') refers to fps for what we've been calling the 'delay', rather than the other frames. xP Silly me.
Your directions are very clear, this is just in case anyone wants a bit of translation:
Red box: (fureemu) Frames
Teal Box: (byou ni henkan) Convert to seconds
Blue Box: (jikan) Time
Box above Pink one:
(byou mae kara kaunto kaishi)
lit. Count start from before the (targetted) seconds
Pink box: (A little unclear, something that starts with "byou hayaku kaunto".../fail)
omote id wo nyuuryoku shitekudasai
Since omote does roughly translate to surface or face, it looks like they're asking for your OT ID number.
"ID to irochigai no seikakuatai wo nyuuryoku shite (kenshutsu)
They're asking for you to input the personality value of the "different colored (pokemon)", which I assume is the PID of your shiny Pokemon.
It does look like a secret ID check, you're most likely correct.
ポケモン裏IDチェック stands for Pokemon (reverse/under) ID check.
Alright, moseying off~