1) He means you need to copy the entire file (msgres_4004_1001.txt) as it is into your skin's folder
2) The reason you need to use 59000 or higher is because the other IDs are not available. You can use whatever ID you like but it must be above 59000. Don't forget to add it as a new image into your SkinInfo and copy the image into your skin's folder.
3) If you don't replace the file into your SkinInfo, Messenger will load its default file. Replacing it will force Messenger to load your file. The name you will specify on the SkinInfo must be the same as the file's name. In our case, it must be msgres_4004_1001.txt
Also, read the Skinning Documentation again carefully. It explains pretty much everything you need to know.
This page has very useful stuff also