So I checked the Activity Monitor, so far nothing out of the ordinary... (I think). CPU for Safari (more or less around) 100.7, CPU Time 1:22:59, Threads 27, Idle Wake Ups 5... Memory for Safari 6.98GB so far, Compressed Memory 0, Threads 23... etc. Energy 100.6, Avg Energy Impact 102.31...etc. Disk 280 MB, 64.0 MB read...etc.
I still can't shut down Safari without hanging
I tried what you suggested with the CMD Shift 3, still hangs.
The weird part though is that I noticed my history stopped registering sites visited. This is very weird. I tried looking up something I browsed and the history folder is completely blank. The url bar also cannot remember previously visited sites even when I visited them 1 minute ago.
I'm thinking something happened when I used CleanMyMac 3. Also right now, the CleanMyMac 3 app is telling me I only have 2.57GB memory left out of 16. I can't figure out what is eating up all this memory! Nothing is running except Safari.
I usually clean my computer with CleanMyMac once a week over the weekend. This cleaning usually consists of:
System junk (removing temporary files to are up space), removes unused binaries and localizations, getting rid of various broken items and leftovers, removing supporting data from photos, removing local copies of mail attachments, remove unused iOS data from Mac iTunes. I've been doing this for years with no issues. I also feel it speeds up my computer.
Then once a month I use also CleanMyMac to do Maintenance such as:
Running Maintenance Scripts (rotate system logs, remove temporary items, flush DNS cache, speed up Mail by reindexing the envelope database, rebuild launch services database, reindex Spotlight, Repair Disk Permissions (repairs broken file and folder permissions), and Verify Startup Disk.
The only thing I did this time is I also did the Privacy Maintenance which removes my browsing history along with traces of online/offline activity but my new history should be there by now and it's not.
Either something happened while I used CleanMyMac (although I find it weird cuz I've been using it for years) OR I did a system update on the same day this crap started happening. The update was for the OS through the App Store.
Can't think of anything else :/