Sims 3 can be quite a pain to install but once you get the process down it gets a little better. You can't keep your Mods folder (containing the CC /hacks) in the game during patching. Every time you patch you must remember to take that out, patch, then replace it. If I remember correctly custom sims are normally .sim files and go in your "saved sims" folder. They will appear in game but (somewhat similar to TS2) may not appear the same unless you download the additional skin textures, sliders, and touches like eyelid enhancers etc., that the creator used to make them. It's not as bad as them being invisible if you don't include the textures they will just look different--but not always in a bad way.
The "Framework sounds more complicated than it is. Just set the files up in the correct path as seen below. I used these to help a friend a while ago so if it helps:
Delete these before running game after adding in new mods/patching:
ignore that my package files may look different than yours due to Sim3pe they're still just package files.
Inside the mods folder:
The other part of the framework that is needed is the "d3dx9_31.dll" file and it goes here:
You can place the master controller where I have awesomemod. I use some of Twallans mods too inside folders in here but only recently started using master controller along with AM. It's a bit more complicated for me to use so I use the one I find easier (AM) until I master the other so to speak.
The main thing is similar to what Mookie said, set up the framework correctly & make sure the mods are up-to-date with the current patch level.
I can't say much more since I recently revamped my computer (uninstalling all the of Sims 3), got a new one with the ever annoying windows 8.1 and like you am in installation mode (x3). I have all the Sims 3 EP's and most of the SP's but in over-tired frazzled mode it's hard to remember all the steps. It's complicated but I have to say very worth it (from a pets and mermaid lover POV
). I wasn't a Sims 3 fan since the beginning but the pets, supernatural and Isla Paradiso EP's made me love it--especially the horses. I could do without the zombies though (lol, sorry Mooncat:P ) but thankfully there's a mod to prevent them from spawning so I get to have an undead-free game.
I'm still a diehard TS2 fan and (am reinstalling that as well) but Sims 3 has made it's way into my heart.
I'm sure this will help someone else down the line as well. If I can think of more I'll add it for you.
*ETA: Read your update after I posted, multitasking here as usual. I bypass the launcher to play and just use mostly package files which I put in the mods folders. The exception is custom houses which I install with the launcher. Origin is not something I use so I'm afraid I can't help with that.Last edit: added missing program files framework info.