The only thing I miss sometimes is you can't manually add passwords.
What's a "java ghost script"?
And, yes I do close all browser windows/processes before login, and after logout of important websites for instance to make sure cookies and passwords are gone from browser memory.
Correct.
Firefox at least offers you the ability to set a master password to encrypt all the rest.
Your Google Password is also available to Google. (At least every time you log in, even if they properly hash and discarded it after authenticating you and just use a token from there.)
I highly suggest you read chrome's privacy policy on that password sync feature. Hint: when enabled on android the wifi password is unencrypted (or reversible, which is close to the same thing. they claim it must be so to work with wear)
I sync with Seafile over WebDAV.
I sync my phone using Syncthing, so that's one way.
Then again, a password storage solution is probably investing so much more into security that it may be actually better than using something else..
OTOH you're losing entry-level syncing which is quite the inconvenience...