@operajunkie4 All your existing user data is in Documents > Electronic Arts > The Sims 3, so you can copy that entire folder onto your new computer and have access to everything you might want in the future. If all you want is your old saves, you can just copy the contents of the Saves folder; saved households and builds are in Library; sims saved in CAS are in SavedSims. But downloaded sims/households/lots are also saved to these folders, so if you want to start clean, without any bad custom content, it may be better to move over your saves and nothing else, and save fresh copies of any families or builds you like.
For the NRaas mods, I'm sure you have a list in mind, but my list of game-saving mods is ErrorTrap, Overwatch, MasterController, Traveler, Register, and Traffic, with other mods being incredibly useful in many situations. And of course the NRaas forum is a great place to ask questions about their mods.
I don't know what manager you're using for custom content, but if it's CC Magic, I can't really help you there. A lot of people swear by it, but others have trouble rooting out bad cc or just find that the game won't launch unless CC Magic is disabled. If you like it and are comfortable with it though, there's no reason not to use it. Just keep backups of all your cc in case you ever want or need to revert.
For the bad cc that sneaks into other downloads, the best strategy is to keep it from contaminating your game in the first place, especially since it can be so difficult to get rid of. I'd never download anything and put it straight in my main user data folder. Instead, I test out everything in a clean folder first: I move my Sims 3 folder out of Documents\Electronic Arts, open the launcher to spawn a clean folder, install whatever it is I want to look at, then check the installed content in the launcher for stowaway items. I also use the cc in-game so I can see whether it works as intended. If everything looks fine, then it's okay to trash the new Sims 3 folder and add the content to my main folder.
This isn't a totally perfect system because some cc only shows itself in certain situations, like the heels that give babies the Grim Reaper robe. So if you want to be extra careful, you can create a household with sims in different age stages to test with, and leave that household in a testing folder that you only use for new cc. The main point is to look at everything you download separately, before it has a chance to infect your main folder.
As far as organizing goes, I think you can go four subfolders deep for custom content. Some people organize by category of item (e.g. clothing > YA female clothing > formal), and others go by creator. There's no one right answer; whatever works for you is fine.