Is that still the case? Every page I visit seems to work with https, but I often have to prepend
https:// to the link URLs manually, after the site tries to redirect me to a non-ssl page. I would suggest to update the links throughout all the sites so that if one is connected with https, they stay there. I make this suggestion with all due respect that the sites are awesome, and that it may not be a simple, easy task; just pointing it out!
I don't have enough points yet in the meta site to answer several questions about HttpsEverywhere; but it seems like their problems are not the whitelist, or any other plugin, but that the links on Stackexchange forums don't correctly link back to https.