So I have finally found a solution that works for me. Just thought I would update you guys.
My main objective of the kindle is to Read Articles, that I select to read later. I have installed the "Save to Pocket" Safari extension and I use that to save my articles
Once I am finished reading my list, I use Calibre to download Pocket articles using this Recipe ->
http://fossies.org/linux/calibre/rec...itlater.recipe
(I changed the Minimum articles to 1, dont know why the script specifies 10)
Then I simply Sideload the articles using the cable and it works pretty well for me.
Next step is to somehow get this on my server and use it to push the files to a directory, which then my kindle syncs and deletes once downloaded
Will let you guys know of my progress
PS: Have been a part of many forums(unrelated to kindle), and this is one of the more helpful ones for sure.