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) Acquire pokemon roms (you should own a physical copy, btw...), place them on the R4
3) Patch your NDS pokemon game(s) with the pokepatch. The V5 alpha worked better, I think.
4) Launch the GBA Exploader, load the ROM in NOR mode (R and L buttons to switch modes) by selecting the game and hitting 'A'. This will take a while at first. Then hit 'Y' to launch.
5) Play your game as far as you'd like, until you'd like to transfer over some pokemon. Save and restart your DS.
6) All should be good: launch your patched pokemon game, select the transfer option from the title screen, go to the pal park, etc.
The nice thing about this method is that you can easily switch back and forth between playing your gba and nds games. There's no need for running save files through an emulator or running separate apps each time. Good luck!
