I am having trouble uploading HTML files via FTP (using SSH) and ASCII mode. It seems that the HTML files are not being transferred in ASCII. The file extension is html. When I go to FTP->Edit Site List, the Misc tab is grayed out. Is ASCII mode not supported for SSH FTP? 
I don't think ASCII mode transfers are part of the SSH protocol like they are with FTP. Files are simply transferred as-is.
You could run an end-of-line conversion tool on the files before transferring them if software at the other end requires Unix EOLs.
Of course, you could also ask GPSoft if they'd consider adding the option to emulate ASCII mode with SSH.
For what it's worth, all of the Unix-based and Linux-based web hosts I've used have worked fine with Windows-style EOLs. I upload files edited on the PC via SSH without having to convert things. If I need to edit a config file or whatever that needs to keep Unix-style EOLs then I download it via SSH and edit it in something that preserves the existing EOL style, then upload the modified file. The only problem comes with new files (some text editors have an option for them though) or editors which always save Windows EOLs.
I was using SecureCRT and it supports ASCII transfers. I'm not sure how it does it, but it does. I may just go back to using that as it may be the best option for my needs. Hopefully ASCII transfers can be added to Opus.
I know I could just stick with binary, but that causes some complications.
I was also a bit disappointed that key authorization wasn't supported with SSH.
But overall I still really like Opus and am still learning to work with it to get the most productivity out of it.
Key authorisation does work in Opus, via PuTTY/Pageant. I use it at work.
The only drawback at the moment is you'll still be asked for a password but if you just hit return the key that Pageant has in-memory will be used and everything works. Hopefully that will be improved in the future.