Okay, I restored the original post as best I could be arsed to. Some download links are dead, and the skins section was all over the place so I scrapped it completely and only left a few download links (besides, the default skin is good enough ).

Here it is:

Warning: Spoilers inside!

Moonshell 2 FAQ, Guide, and Index
by KingdomBlade
​

I will begin to give everything you probably need to know about Moonshell 2.


Rules are:

1. No spamming
2. No flaming
3. If I have missed anything, be patient and I will add it.


Table of Contents

About Moonshell 2
Setup Guide/Instructions
Wallpaper Making Guide
Tips and Tricks
Bugs, Limitations, and Troubleshooting
Frequently Asked Questions
Splash Animations and Sound Effects
Thread References



About Moonshell

Moonshell 2 is by far the most advanced media player for the DS. This application is the successor to the original Moonshell. The author of this application is called Moonlight (or Infinite Paralyser originally). Moonshell 2 currently supports the following file formats:
-Music Formats: MP1, MP2, MP3, OGG, WAV, M4A, AAC, WMA, TTA, MID, RCP, R36
-DPG encoded video
-MOD formats: MOD, IT, MTM, S3M, XM, 669, MED, STM, AMF, GDM, ULT, UNI, ASY, IMF, OKT, STX
-Chiptune formats: SPC, NSF, GBS, HES, AY, SAP, KSS
-Playlist formats: M3U, WPL
-Picture formats: JPG, BMP, GIF (non-animated), PNG, PSD
-Text Files


Setup Guide/Instructions

To install Moonshell 2, first, download the package. Then, extract the package with an archiving utility. The most commonly used are 7-zip, WinRAR, and WinZip. You should extract it to somewhere with easy access such as the desktop. Then DLDI patch it if needed. (I turns out that this is the only application that needs DLDI patching with the TTDS). Insert the Micro SD Adapter into a USB port. Copy the moonshl2 folder onto the root of your Micro SD Card, and place the monnshl2.nds anywhere on your Micro SD card.After that, safely remove the hardware, and open your DS. Open Moonshell 2 now, then it will automatically prompt you to change the language. If you need to change it later, just open Languageselect.exe from you computer. To install Moonshell 2 as your R4's default media player, rename moonshl2.nds into _DS_MSHL.nds To set it as your CycloDS default media player, create an new folder on the root of you card called moonshl. Then rename moonshl2.nds into Moonshell.nds. It will can now be accessed from the center button.

Keys

Keys

Keys:
X/Y: Configure Volume
A: Open File
B: Return to Previous
SELECT: Launch Tabs
START: System Menu
L+X/Y: Configure Brightness
L+A/B: Previous/Next Song
L+R+A: Play all tracks in SD Card
L+Left: Show MP3 Controls
L+Up: Pause
L+R: Pause
L+Down: Toggle Playback Mode
L Double Tap: Previous Track
L Double Tap then Hold: Seek Backward 1%
L Triple Tap: Pause
R+Left or Right: Seek Back/Forward by 1%
R+Up or Down: Seek Back/Forward by 5%
R+A: Play all Tracks in Folder
R Triple Tap: Standby Mode
R Double Tap+Hold: Seek Forward 1%
R Double Tap: Next Track

Tips and Tricks

Tips and Tricks

Dust Box
Create a folder called Dustbox on the root of your card. Then, when you delete a file by pressing START, it will end up in Dustbox. Think of it as Recycle Bin.

MoonMemo
MoonMemo is like a notepad feature. If you create a folder called Moonmemo on the root, you will be able to access memo mode from the System Menu. You can jot down small notes here.

Taking Screenshots
To take a screenshot, just press select and hold for a couple of seconds. It will be saved as a bmp file but it will not be saved if there is not enough space on your card.

Remove Shortcuts from the Launch Tabs
Press and hold the item, it will be automatically deleted.

Install Skins
To install skin, simply open the skin file.

Install Wallpapers
Open the image, then press start. It will be set as your wallpaper.

Remove Transparency to bottom screen when Applying Wallpapers
Press start when viewing any image, then uncheck "Apply transparency to bottom screen", then set said image as wallpaper. You can switch and the option will still be active.

Installing a Splash Animation
Place the splash.ani in the Moonshell 2 folder then replace the old one when the warning pops up.

How to Make a Wallpaper

How to make a Wallpaper

The simplest and most easy to use free image editor is paint.NET so get it here.

First, you should choose a theme of any flash cart from any website like except for Acekard because of the calendar. I chose a GBATemp Cyclo Skin.




Then extract the package anywhere. Open paint.NET and make a new picture that is 256x384(without border) or 256x450-460(with border)




Drag the file extracted that you want for the top into paint.NET. Then choose "Add as new layer". It will appear like this.




Then, drag the one for the bottom then do the same, it will appear like this.




Adjust the position so it fits perfectly at the bottom. It will be like this.




There you go! Just save it and done. Of course, you can resize your own images but that would risk quality.

Bugs and Limitations

Bugs and Limitations

v2 can't see hidden folders
There is a problem that it cannot be opened with the R4SDHC and EZ4.
Unable to extract misctools folder using Windows due to file/folder corruption
Moonshell may flash up card/DLDI errors but the messages will disappear

Music format limitations
NDS: Not support commercial NDSROM files.
WMA: Not support 'loss-less' and 'voice mode' format WMA files.
M4A, AAC, WMA: Not support encrypted files.
MID: Not support 'Standard MIDI file format.2' format.
SPC: Tone quality is very bad.
Chiptune: Only the first track is performed. The FM sound chip cannot be emulated.
Playlist: Support encode is ANSI, S-JIS, UTF-8, CP437, CP850, CP1252.
Text file: Support encode is ANSI, S-JIS, UTF-8, UTF-16BE, UTF-16LE. Auto detection only.
File size limitations
Picture formats: The size that exceeds 3648x2736 pixels cannot be displayed.
Text file: The line that exceeds 131072 lines is disregarded.
MOD: The file that exceeds about 500KByte might not be able to be reproduced.
MID, RCP, R36: The file that exceeds about 500KByte might not be able to be reproduced.

Fatal Error occurs when using thumbnails in 1-Line Mode.

For the full fatal error list in Japanese, click here and one translated with Google Translate here
So far, there are a few problems caused by the disk check.

Frequently Asked Questions

FAQ

Q: Will it work on [insert cart name here]?
A: It will probably work on most carts, but, as it says above, it may not work for the R4SDHC and the EZ Flash 4. It may also not work on some other flash carts, so if you find it not working on yours, post it here.

Q: How do I convert videos for Moonshell?
A: There are multiple ways to do this, but most people prefer to use the converter bundled with the package.

Splash Animations and Sound Effects

Splash Animations / Sound Effects / Wallpapers

Splash Animations / Sound Effects:

PS3 XMB: Topic.
TWEWY Sound/Splash: Topic

Wallpapers:

M3 Sakura Wallpaper Thread (Although these were made for M3 Sakura, they will also work for Moonshell 2.): Topic

url=http://ms2blog.blogspot.com/
http://www.mediafire.com/download/zyok2zjwmvn/WallpaperPack1.zip
http://www.mediafire.com/download/zwxydnytmjx/iWallpapers.zip

References

Moonshell 2 translation thread
GBAtemp Wiki
Commercial ROM Loading with MoonShell 2 & YSMenu Guide
Commercial Rom Loading with Acekard 2i Guide Toolkit(includes, DPGenc, Skintool, Make splash.. etc.)
M3 Sakura Skin Tester (Although made for M3 Sakura, will work for Moonshell 2. For screenshots, go here.)
Videos on Moonshell with BatchDPG Guide
Wikipedia entry.
Video conversion on Mac