Kasutubh
I think Dana gives some great places to look. The first place to look from my vantage would be Google Analytics (GA). I would go back to the good old days and start moving forward to find what happened when. Especially if you know you made change one on day one, change two on day four.
That said, I think it is a cautionary to any who are changing site structure/architecture or anything within the realm of UI/UX that results of changes can only be tracked to the degree that a single variant is isolated/isolatable. (Yes, there could be an argument to this-I am speaking broadly).
By making one change at a time, you are able to insure you have no oops moment that is lost in 5 changes of redesign.
I would focus on what most likely effected the ability of the user to get to the site. Did you change meta descriptions, were any outside the site changes made; do you advertise somewhere and now have halted it?
At the end of pondering I keep coming back to the ad changes and am wondering if the look of a month ago and now is so different you are getting people to the site but they are not going deeper (analytics will tell)? OK I have a thought. AH HA:
Using the wayback machine, I looked at home page cache from July vs Now. I like July 100% better. (Dana, don't think it was the tag cloud even though I am not much on them.)
I think you have messed with a UI/UX issue and need to slowly step back. when I look at both pages I just do not like the look or feel of the new. It is sterile, too news oriented. There is not a community feel at all. On July cache I have the FaceBook app showing people who are a part of your community (a good example of this is a site called SEOmoz), below that I have what an engineer said. They get to be involved. I was just looking at wired magazine and I had no sense of community but I did not pick it up for that. Here I came for community, saw a question that intrigued me, liked what Dana was saying and wondered if there was anything I could add. THINK ABOUT IT.
If I had to place a $100 bet right now, it would be that this is where your problem lies.
I hope this provides some direction,
All the best,