I can now report success! It took a lot of guess & check, there really wasn't a simple, straightforward guide for the R4 + EZ-flash V 3-in-1 + pokemon.
In case anyone else could benefit, I'll line out the steps.
1) Get the GBA Exploader (I used 0.58b), place it on your R4 (it's an nds app)
2)...