HeIIace As they say, been there, done that, many times, including things you're reporting. This is not a mod issue; it's a CC issue most likely. With every update, there is a potential that something that was perfectly fine will get broken by the update. And it certainly looks like that is what has happened to you. While that is probably what you're dealing with, I do suggest you run a repair. Delete the localthumbcache before you start the game again. As good practice, you should delete that file from time to time so your game will update the pics for your CAS and build/buy objects. And always delete it when you make large CC changes in your mods folder.
Simply removing files that you think might be broken is not enough. You need to look at each CC item individually to find what is causing the things you're reporting if you really want to fix the problem, particularly if you have a lot of CC. You can use the 50/50 method to find the files but since you have several things going on, it's better to go the test everything route imo. It will take a lot of time if you have a lot of CC. So, I suggest you look at your CC individually, one thing at the time, in Sims4Studio and check the tagging and to see if it displays properly. You'll probably be surprised by how many things you have that don't even show up in game. I'd start with any CC eyebrows and skin tones you have. One thing you need to be aware of though is that default replacement items will not give you a 3D view in S4S and you will break them if you run any of the autofixes in S4S on them. On the skin tones, if they are old and made before Island Living, you need to check for updated versions as IL broke all earlier skin tones. The grey undies showing up under outfits in CAS is usually one of three things. Either you've got a CC accessory that looks like undies, CC undies that are tagged as a bathing outfit (either full body or separates) as the bra under the swimwear is not a game item, or a broken undie file which is displaying incorrectly (I've had all 3 at one time or another). Anything you find that is not working should be updated where possible or removed from your mods folder.
Hope this helps.
Info: luthienrising