Put in _rpg and AKmenu without deleting anything. Put AKmenu in where your roms are and it'll show as a nds file.
AKmenu will show up as a normal nds game on your R4, you don't need anything specific, but you do need to change the name of your sav files.
Steps to installing Wood R4: Back up everything on your SD card. Format the SD card. Place the menu file and the _rpg file into the root of the card. Place all your homebrew and roms and other folders back in, but NOT the old firmware files. If it still doesn't work, you are NOT using an original R4. Also, please say what firmware you are running on your R4 so we can confirm if it is an original R4. If it is an SDHC or anything other than just a plain old R4, there is no solid way to get Wood R4 working on it.
A lot of the time issues will arise after switching out firmwares completely that can only be solved through a format. It is better just to be safe.