Firefox corrupted the file I download. Upon fix with reset or uninstal, more problem happened

This all started 5 hours ago, when I tried to download a .doc file from my school website but Microsoft Word opened it with "file conversion" options and the preview is filled with unreadable codes. I was using Nightly 64-bit on a newly installed Windows 8.1 64 bit system (about a week ago after I upgrade my ssd).
1. I tried open other .exl file from the same website, but Microsoft Excel could not open it at all saying the file is corrupted. I used IE 11 to download the same files and it worked perfectly. Problem with Nightly it looked like.
2. I reset Nightly then tried to download the same file again, not working. Tried safemode disable all addons and try to download the .doc file. It surprisly worked!. So it seems like an addon problem. Then I disabled all addons manually restarted again but tested not working. I was really frustrated at this point so I believe my Nightly was hacked by malware or some hidden plugins.
3. Uninstalled Nightly then I cleaned all files left with Ccleaner. I checked full scan with Windows security essential; downloaded malware cleaner "Malwarebytes". Yes a few malware like files were detected and cleaned up.
4. Downloaded waterfox 64-bit but now more problems appeared. It still cannot download the .doc or exl file now. The right click menu is not showing up at any webpage, image or highlighted texts. Ctrl+click link to open link in new tab is not working, just nothing happens. I try to reset or safemode restart, Nope! the help menu is gone, perfectly clear!
In brief, I would not like to reinstall my OS for this issue. I wish I could find some software remover that detects firefox virus pluggins. I don't want to try the 32-bit version of firefox for this issue.
Thank you.

Thanks for the fast reply.
I deleted everything, and download the official firefox 32-bit and tried your advice disable everything. Yes it worked! it brought up the help menu.
And the word document is working as well after I could 'help-troubleshoot-rest firefox'.
Thank you very much. I think it was the Nightly setup naturally not compatible with .doc links. It also messed up the settings for my waterfox/firefox which I downloaded later.
However the right-click menu is still not normal. nothing shows up nor I could open up link in a new window. This did not happened in Nightly as I stated in the original question. Any suggestions?
Btw. After this I might stay with the official firefox 32-bit for now. is there any performance difference with 64-bit or compatible issue with Windows 8.1? I know that 64 bit firefox is not released yet.

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