First up, ouch - jut Raikou left is going to make your job difficult as verifying your delay is going to take a lot longer. My sympathies on that front.
One solution, if you don't have issues with doing it, is to use an action replay to reset the flags for the roamers and re-release them in order to speed up your verification processes and let you reset trying faster. That's only if you don't mind hacking your game slightly. If you don't have a problem the codes are here (You want the Entei/Raikou one and the Lati@s one):
https://sites.google.com/site/pokencg/rng/howto/emu/ar
Your delay is not going to be thrown off by anything in game, and as far as I can tell everything on your setup is fine - I can't see your EonTimer (or similar) to be sure that's set up right, but if you're missing by between 5 and 12 it sounds like it (I assume you're getting odd delays on your misses). You're going to have to keep trying at it, the timing is something that comes with practice.
Don't sweat it, it is more than possible:
Hi,
You can download/install brew, which allows you to install packages very easily.
Once you have this installed, you can install Wine by typing brew install wine
into the Terminal.
Once it's installed, you should be able to run the 3DSRNGTool by navigating to the 3DSRNGTool.exe directory and running wine 3DSRNGTool.exe
https://play.google.com/store/apps/details?id=com.dev47apps.droidcam
it has the option of wireless but it's definitely better to use it wired, it'll drain the battery. i also got a gooseneck to clamp to my desk and you'll be able to have the camera pointing at your switch without you needing to hold it up
https://sites.google.com/site/pokencg/rng/howto/txt-p1
edit: omg just realized how horribly out of date this is... it's 2+y old.
you'd best ask for what aspect you need help on, not a generic "help pls"
if emu abuse you will have a hard time
1) download a program called runasdate (from here http://www.nirsoft.net/utils/run_as_date.html) and open desmume with that it allows you to set a date/time without changing pc date/time and makes things a little easier
2) use the time from seed to time window
3) dont use ram watch it slows down the emulator use this lua script you need the lua51.dll's mind http://pastebin.com/95VmQpH1
This one: https://play.google.com/store/apps/details?id=com.rise.automatic.autoclicker.clicker
I had to experiment with manually editing the timing of each button press to make sure it registered and didn't get out of sync with the switch. I wound up using 100ms for length of button presses and between button presses to move across the date fields and change the day of the month, and 200ms when pressing the "okay" button or pressing "a" to re-enter the date setting. (Tap on one of your recorded tap indicators to edit the timings)
You set the delay between loops and the number of loops to do on the main screen.
Doing it the way I was, you are only changing the day of the month, so the frame that loops back from 31 to 1 doesn't actually seem to advance the frame in game. But then continuing from 1 to 2 and so on seems to resume frame advances.