I thought I would share what I found regarding getting wifi linking to work on my DSi and 3DS for those that are interested and haven't gotten it to work.
Basically what I found was that for these two systems to connect I had to have both run the DS build. No other combination of builds worked. However, I've heard people getting it to work by using two DSis and the DSi build, but I don't have the consoles here to test that.
I tried to make a guide on how to set it up on the wifi link compatibilty list which I've also updated with the few games I tested:
https://wiki.gbatemp.net/wiki/GBARunner2/Link
I went on to test a couple of games and found some weird things. The most surprising was the fact that in order to get Advance Guardian Heroes to connect I had to first make the systems connect in Contra Advance and navigate back to the rom browser and run AGH.
Next I found that AGH has an extremely stable connection. I went 4+ meters away across the room and the systems kept being connected and I could even play without noticing any latency while looking at the other system's screen.
This is not the case for every game and most games I tested did not work, even some that are reported as working by others. This makes me believe that compatibility is tied to what systems you're using and what build. Most likely AGH is a single exception to how well linking works. Still, there are many games that have not been tested.
I might be able to test 3DS to 3DS connection later this summer and I'm curious to see how that goes.