I did forget to mention that the 1541 ROM, BASIC ROM,KERNAL ROM,CHAR ROM and Frodo.fpr need to be in the rd folder :o
In case that isn't it, I've attached a version that other R4 users have got working. I forget which version it is and weather you can alter Frodo.fpr(frameskip and whatnot but I included it anyway),but it worked for them.
It is all set(prepatched), just download and extract directly to the root of your card.Boot it up, Press left shoulder button, choose test.d64 with the A button. Press Right Shoulder to auto load first program. It should be a menu. Press "1" and return. This is a program I know works on my DS. It may require you to change joystick ports, by using the Select button.
Hope this works for you guys.