After countless hours, I finally got the program to work. Key elements are to leave ALL files in the RD folder...it doesn't matter if Frodo DS is on the root of the SD card, but everything else needs to be in the RD file.
If you can find it, use Frodo DS 030507. So far, that's the most steady version I've found. Then, using notepad, open the .fpr file. Scroll down and remove "Maniac mansion"...just leave the area past that equal mark blank. Scroll a little further down and set 1541 emul to TRUE. Save the .fpr file. Patch Frodo DS using the R4 DLDI patch program.
When you put the SD card back in the R4 and start the emulator, go to the RD file, select your game, and hit the right side button. This will load the game in 1541 mode and pretty soon you're off and running!
Supposedly it works without 1541 emulation "on", but this being on is the only way I've gotten it to run at all. It's a little slow right now, but I have not tried adjusting anything else yet.
Hey, so it's a little slow...it's worth it to play Pogo Joe on the DS!