5) I currently have a usb drive that has a collection of Classic Mac files from a different Classic Mac by someone other then myself, which read as locked unix Executables. Which when moved through the shared folder(which descends to the Desktop). I have been trying to get these files to open but the OS can't find the application which created them. I believe this application is Microsoft Works 3.0 which is another locked application on the desktop. I am aware that i can't run applications off the desktop due to a known bug but it's locked as well so I can't seem to move it to somewhere where it'll work.
What is the current path of your shared folder on your host system?
It sounds like your current situation is (correct me if any of this is wrong -- unlike Ronald, I actually slip into condescending language from time to time, but not intentionally):
You have a USB drive that contains a bunch of data forks of files copied from a classic Mac. On your host system (running El Cap), these appear as locked Unix executables.
If this drive is formatted FAT or EXFAT (or anything other than HFS+ really), you've lost all the resource forks and Finder Info metadata. This is not recoverable. The files on the drive that only had info in the Data fork, however, may be recoverable.
You have set up SheepShaver with a shared folder. Where on your host system is the shared folder pointing? It should be somewhere on the root drive, and you copy the files from the USB drive to this location prior to starting SheepShaver.
Once you've started SheepShaver, you can open the Unix "disk" and drag the files onto the OS 9 boot volume disk or a folder inside it. If you just drag them to the OS 9 desktop, they're still in the Desktop folder inside the host shared folder and did not get copied to anywhere useful.
Once those files are copied to the OS 9 boot drive, you'll still have problems opening them, as they've lost their file type and creator. You will need to add these back using a tool like ResEdit, ABetterFinderInfo, FixFileT&C, or similar.
Applications copied over from your USB drive will not work, as you don't have the resource fork, which contains the executable code. However, you can download replacements for those properly enclosed in Stuffit archives or disk images from places like the Macintosh Garden.
So... having said all this, if you're just trying to open MS Works 3.0 documents, you might be able to do so on El Cap using LibreOffice. Not guaranteed though; I can't recall what formats of Works it can import. It CAN import ClarisWorks/AppleWorks documents.
Files that are locked can be copied even if they can't be moved. If you can't copy them, you've got a file permission issue (the files belong to a user other than you). This should be overrideable for external USB devices from Terminal.app by doing sudo cp <file> <destination>. Getting info on the files and changing their owner may also help.