WELL THEN!
Not only was that very explicit and concise, but it worked perfectly. Thanks muchly, samiam144! Every game and save is right there.
So, for those who were wondering how to do something like this, it's almost identical to a normal system transfer, except for that one scary moment.
Basically, once you transfer from your sysNAND of the original 3DS to the emuNAND of the target 3DS with the normal system transfer process, the target 3DS will restart. Now, I tried to force it to boot into menuhax the way you can do when you exit the settings menu, but no such luck. It booted straight into the settings menu of the sysNAND while giving the message "trying to connect to the internet to verify the transfer." (I'm paraphrasing the message).
This is the point at which I freaked right the f*** out. You can't exit to the home menu or do anything during this, but DO NOT WORRY AND DON'T FORCE A SHUTDOWN. Your 3DS will not update, you will just get an error message and be kicked back to the home screen of your sysNAND (It's fine, you'll still be on your original sysNAND firmware.) If you try and boot into your emuNAND from here, you'll be taken immediately to the settings menu where it will try and finalize the transfer, which it will always fail.
Basically, what you need to do after that is boot into your sysNAND (which will allow you access to your home screen) and turn wifi off. Boot back to emuNAND and the transfer finalization process will give you a new error message which will allow you to cancel the transfer. Do it and you should get a message basically saying that your NNID has been transferred and some other words were there, I dunno, it's not important. If you chose the PC transfer option, you need to do exactly as samiam144 instructed. If you didn't, then those files probably came over during the transfer just fine, or something.
After all that's been done, go into the eShop on your emuNAND to start a 5 minute long verification process where -
I think- Nintendo's servers basically register that your NNID and your game licences have transferred to a new system. After that, everything you had before should show up like magic.
The only difference between the method described above and the process described here:
http://hackinformer.com/forum/thread-336.html is that, in order to disable the wifi and "interrupt" the transfer process (in quotes, because the transfer is essentially finished at that point), you need to boot to your sysNAND and use the menu options instead of using the switch on O3DSs. Other than that, same story. If there's one thing to remember, it's that when it boots into sysNAND and connects to the internet, don't freak out and turn off your console. I don't know what that would do, mind you, but it's unnecessary.