1. it should only have 4 .cias missing im not sure what your looking at here
1b. you could patch the agb yourself (in rxtools this is no longer need to do this)
1c. and firmware.bin . . . as far as i know that is a file used to run rxtools and rxtools comes with the files needed to generate it
2. dsi section? you mean on that iso site? and no its not needed (most of these files you are asking about are upto here only in the update download page to fix the update if you did not pick the modified file of .cias in case you for some reason wanted to update to 8.1 from 4.2 and still wanted the old MSET (System Settings) app, NDS flashcard whitelist, AGB_FIRM (for GBA games), and TWL_FIRM (for DSi games) )
3. nope you dont need to download spider anything just the update pack of .cias "same as above (assuming you are using the modified pack)"
4. im not sure which cfw is best for this . . . i have no idea personally ive only done this process with (rxtools 2.5.2) the link i previously posted may have more info on the update process
5. pasta cfw "i believe its one with rxtools now (the rxtools menu says "rxtools with pasta") " (the op will tell you to use rxtools as it is newer) / cakes is more feature rich than rxtools but to accomplish this it has a hand full of plugins(in .cake format) that you will need to setup / reinand ive never looked too far into "sorry idk what makes this cfw unique" / rxtools the most recommended cfw (and the one i picked the main reason i picked it is because while i read up on updating emunand for playing new games, i noticed updating emunand has never really been a problem with rxtools "in fact the day i set it up nintendo released a new fw version and i updated emunand to that with no problem") / ntr cfw is unique to the others as you can use it on top of other cfws (to add its features to your current cfw "like playing out of region games with a higher compatibility rate or using
cheats") / others=??? idk if there even are others out there lol
edit i think it reads better now
sorry you know its a shame this is the only language i know and i still suck at it