I'm not sure how much of a walk-through you'll get on here... but maybe this will get you in the right direction. You mentioned a dldi patch, and that's probably all you need.

My DLDI patcher is called DLDIrc and worked well for my R4DS. The M3 Simply is virtually the same thing, but uses slightly different firmware.

http://forum.gbadev.org/viewtopic.php?t=12292

There is a link in the post on that forum. You can install it and choose the correct DLDI driver to use. Once installed, you can right click on any .nds file and you'll have a menu option added to your right click menu in Windows to patch it. Then a dos window comes up, you hit the space bar a couple of times and viola, you're done.

I can't be sure if this is what you need to do, but for a good DLDI patcher, it works well for me.