before everything, do not format your 3ds. as long as you have most of the .sav files, you can maybe restore them. and that might be only possible if you still have the "keys" to encrypt all games as they did before. if i read it correctly, the "key" changes if you format the 3ds. i wouldnt get rid of all the other recovered files yet, but i hope we dont need them anymore. the only problem i see here is, we dont know which save is for which game. means, you probably need to copy (and remember to copy, do not move them... just to be said) and overwrite a save file until it can be recognized from the game. could be painful but it might be worth it. otherwise, the question is which games are really necessary to get the saves from, you might just download 100% savegames and edit them with a save editor. another question is, do you have a list of all games that were installed? or do you remember them? and do you know if there was other important stuff that needed to be installed somehow? the easiest part is to just download all games as cia again and to install them. it would be harder to figure out which .app or other files would belong to which game and thats why the .sav files are the only important files for now.
after all that... to answer your questions:
0. what do you mean when you say "make his 3ds even better"? like install more helpful tools or anything else?
1. and what exactly do you mean by "without the storage needing to be double"? do you mean something like remote install so you dont need the cia on the sd card to be installed, but you can install them from your computer (like ftp or something)?
2. by snes, gba and genesis you mean emulators?
3. you probably will only use the files in the folders since the folder path was not recovered, thats why there are so many files with "_1_2_3_4..." and so on... so if you meant folders directly, no. if you meant the files, yes.
4. we care about the sav files later.
5. if you have any cia files, you can put them on your sd card and install them with fbi. or at least check what cia will be installedwith fbi and install them if you want them installed.
6. yes, you should download all games again.
7. if you want to install cia files that you still have on your 3ds, you can put them on his sd card and install them.
8. if you mean by your sd card not the one from your nephew, you can check with checkpoint which games are installed.
9. and if you want to know what folder the games are located on the sd card... im not sure if it helps since that are all files with "00000001" and i dont even know if the title id is somewhere to see. they are not that easy to figure out.
if you have any more questions, ask them first. i would say we start with setting up the sd card again and check if the sd card is not causing boot issues anymore. after that we try installing everything again and at the end we try recovering the saves and maybe more.