Not sure I can answer the readme files question, as those files are within each PND, so short of following the idea of accessing the PND files contents similar to this but for different reasoning
http://www.gp32x.de/board/index.php?/topic/57912-how-to-acess-pnd-pxml/ then I would suggest using the software wiki's
http://pandorawiki.org/Software_projects to seek the threads, or authors websites for more details. Also see last line of boring post.
In addition on the Pandora itself, the documentation shows up in the menu but defaults to Aora for its versatility of file types it can open but its horribly slow to open and sometimes fails to find anything.
To be honest though I think that much prep in advance is probably not worth your effort.
The Panda happily shifts items about on the card very quickly, even between cards, so if you just have a folder with sub folders of the various game data files stored on the root of the card, you wont be delayed very long to transfer the files via Thunar or the alternative, to the actual appdata folders that are created on first run of a given PND. In fact I wonder if that process mightn't overwrite your pre-prepared folder with the default one its expecting?
Your better off just making the default Pandora folders ED showed with desktop, menu, minimenu folders inside, each containing as many sub cat folders as you wish to organise your PND files with in advance and go from there.
PND's in minimenu dont show in the menu btw, something ED forgot to mention, so you can if you wanted keep all your game/emu files in there, which keeps XFCE menu uncluttered for example. Not how I do things but an option.
In minimenu have a skins folder aswell (not sure if makes it) and have each skin directly within a folder of its own, to get them recognised (not more layers sometimes supplied in the zip, or they crash minimenu until you delete their folder).
As for ROMS create a pandora/media/ROMS folder with sub cats and most of the emu's remember last path, so simply boot each one and point it in the right direction to one game at the top of the list and then exit afterwards. Good to go.
Add music/video/docs folders as required to /media there, to leave the root clean after you delete the empty datafiles folder when your finished copying them to the relevant appdata folder.
Not something you can do in advance but I'd recommend using the keyboard shortcut manager in conjuction with usr/share/applications to right click each apps icon for its launch script and hot keying the apps you'll want most, as it makes it a breeze to launch anything with no menus at all, or shoulder buttons to reach the minimenu tab required to find the icon etc. Simply ctrl+alt+(X)
A couple of hints though,
1 keyboard shortcut the keyboard shortcut app first + and Thunar or the alterative file browser, plus wifi/bluetooth/cpu speed. Plus install Someguy99's script for running minimenu from a desktop icon (see 4)
2 In Thunar drag the folders you'll frequently access i.e appdata, pandora, downloads, media, docs to the left panel.
3 Grab Plengs PND format of CPU speed settings which will give the menu several settings/minimenu several icons. Hot key 800mhz and 500mhz to 8 and 5. Saves messing with the slider or the menus.
4 Copy the relevant scripts for other tweaks people made in the support sections tweak thread and have a folder filled with them ready. Then you can use the terminal from one folder to quickly copy them into the NAND and make them active, test them, then keyboard shortcut the most handy ones. i.e the above mentioned plus the proper OC script if you want to get better speed in some emus and xbox360 pad useage, snapshots or continous ones from within apps/emus etc.
5 Keep that folder for if you ever reflash, so you can quickly restore those fresh, or theres probably a conf file somewhere you could copy that would re-instate your custom settings faster aswell?
6 Bear in mind the panel icons for mail and browser will default to the NAND storing version of mail and to midori which is unstable (as will the menu). Use their launcher scripts from usr/share/applications to point to the correct PND version with SD card storage, or to choose your preferred browser.
6 Have fun (goes without saying)
7 As its a versatile system. Ignore all of the above and do your own thing but as a linux noob, the above has served me well and made any app a few seconds away.
I'll happily post a screen grab of the entire appdata folders if its any use to your SD card prep though, as I have practically every app yet released currently installed?