Some parts or whole body mesh aren't shown in S4S

If the only thing visible are the head and feet, then you're probably missing the mesh to a full-body outfit. These are probably recolors and since most creators ask that the mesh not be included, it wasn't. Go to the website where you downloaded these files and there should be a link to the required mesh on the web page. (If you don't remember where you got them from, just try searching online for the name and the creator. Note: if the CC is from The Sims Resource, there is a tab above the download button, just under the last image, that should say required. It's in a row with the description and the comments. Click on required and there should be a link.) Download all of the meshes that you're missing and then open the items in S4S again to see if that solved the problem.  

Edit: If the CC isn't base game compatible (BGS) and requires Packs that you don't have, that could also create this situation? I'm uncertain, but the web page should mention that.

I'm afraid I still don't understand but here's somethings to double-check, just in case. Edit: If you know all of this already, sorry! I'm just trying to be thorough.

First, if you have any Zip, Rar, or 7z files, you'll need to unzip them. The Sims 4 can't read these files, only package and script files. (S4S can only read package files.) If you need help, search "how to unzip compressed files" or something like that for a step-by-step process.

Second, make sure you aren't nesting your folders too deep. The game only reads 5 folders down by default (counting the Mods folder), so you'd either need to modify your resource file to go deeper or redo your organization process a little bit. I've had CC that didn't show up because I've done that before. Incidentally, Script mods can only be nested one folder down. So mods/scripts/MCCC won't work and you'll need to make it mods/scripts by putting those files directly into your scripts folder or mods/MCCC by placing the entire MCCC folder directly into the mods folder. Package files can go deeper, for example Mods/CAS/Hair/LeeleeSims1 should work. I think one more folder in is also okay, if for example you want to separate the hair accessories into another folder within LeeleeSims1 (it might look like Mods/CAS/Hair/LeeleeSims1/HairAcc when you look at the top of the operating system window) but one more folder within that and it will become invisible to S4S and Sims 4, even though it exists. Double check how many folders you have within one another: one way you can check is by taking folders that aren't visible and placing these folders directly into the Mods folder at the very top to see if they finally appear in S4S. Even if it can't open the files, the folder itself should show up if it can see them. I hope that helps; I'm not sure how else to explain it.

Third, some CC can't be opened in S4S. I don't remember if I said that but for example, true skin tones can't be opened (overlays and other skin details can.) You might be able to open them to create a new project and S4S can modify them, but I've never been able to open and look at skin tones in My CC. As long as you run the batch fix on them, they should be okay and reappear in your game. (There is also CMar's skin converter 2.3 if that doesn't work.) If you're trying to view an accessory that is an overlay for another mesh, you won't be able to see it because S4S can only load one mesh at a time. (Hair recolors show up because of how it's programmed. The hair mesh is called up in that instance, since the recolors is treated as an additional swatch, but overlays like ombres won't really appear and you'd have to try them in game to see if something is wrong. Of note: some accessory overlays only work for the CC they were created for and will look terrible if applied to other hair styles, clothes, or hats that they aren't compatible with.) Anything that only affects game play can't be opened either, even if it's a package file. I'm not saying this is your issue, but pointing it out to clarify that these things might not be broken. If you open a file in My CC, modify it, and then S4S suddenly can't open it any more, that is a problem and the modification most likely broke something, but this is only if you could open it before.

Fourth, some objects are separate. Shoes, pants, skirts, tops, etc. You can't see more than one item in S4S at a time. If you need to see how clothing is layering or if there's some texture overlap between different CC, for example, you'll have to look at those items in the game. If you're only seeing the head when you're looking at a hat, I don't know what that means. I've never experienced that. If you're looking at a dress and all you can see is the head and the feet, that's most likely because the mesh for the dress is missing. Meshes don't go over the body part they're on; they replace that part. In this example, the dress is replacing the naked torso, legs, and arms, but can't find the clothing mesh it's trying to replace them with so there isn't anything there.

Fifth, ALL of your mods must be somewhere in the Mods folder, regardless of how it's organized. There might be some exceptions but that's extremely rare. Lots and Sims go into the Tray folder. Other people's Save files go into the Saves folder. I'm assuming this is what you've been doing, but decided to clarify in case there's any confusion.

Sixth, if you have mods that affect game play, such as MCCC or the Tool Mod, always go to the mod's web site and see if you need to update them; do this after every new update. Even if there isn't a new pack, they regularly add changes in base-game patches. Sometimes it has no effect on anything in particular but that's rare. You can't view these with S4S so it'll never tell you if such mods are broken.

Seventh, after you've made sure every folder within your mods folder is recognized by S4S (even if it can't open those files), just go ahead and run every Build-Buy Batch Fix, then run most of the CAS batch fixes. Ignore the stuff referencing random and different occults for right now; focus on the ones that mention packs and patches. The only one I'm uncertain about is the glass hair fix if you use alpha; I don't know if that ruins alpha hair. After you've done those batch fixes, see if it fixed any of the CC that had these issues. It can't hurt and S4S will create a backup for each batch fix where it changes something. (Note: always backup your Mods folder before you do any manual changes; S4S doesn't create a backup file if you open a file and then change something yourself.)