My site just got a minus fifty penalty

[curioustoddler]

One of my sites is 11 months old. It got minus fifty penalty. I checked. For all keywords all pages are ranking from 5th to 8th page. Site can no more be found with sitename( without .com). It happened all of a sudden. I need help to understand what we did to get this penalty.
In terms of backlinks i did not find anything wrong.Rather i am too afraid of google, i never baught any links. On site we have made lots of changes.
1. On 18th June i made thousands of inner pages noindex.
2. On 5th of July we changed the css, color scheme, site navigation and added google maps. There is not keywords stuffing or anything like that.
Please help me understand what went wrong.
I have read many threads in this forum today and found most of people talking about backlinks as a possible cause for this. But our backlink sources have not changed in last 3-4 months. They are from the same sites.

[MonkeyFace]

Hi tedster, thanks. It was in the link attributes to external sites. I was definitely not trying to sculpt PageRank. The punishment was that my webpage which was on page 1 was sent way back to 16 or 17. That scared me so much I installed a plugin to remove no-index even from the links comments. I disabled hyperlinking in comments ultimately though.

[tedster]

First thing, are you talking about "rel=nofollow" (rather than no-index)?

And second, unless that plug-in went crazy on your site's code, I can't imagine how it would have been the cause of the rankings you lost.

If you were using no-index, it is not a standard attribute so it should just have been skipped over. And if you were using nofollow on external links, that's exactly what it's supposed to be used for.

[MonkeyFace]

Ah, yes "rel-nofollow"!

[tedster]

Well, I'm 99% sure that this was not the cause of your ranking problem, unless the plug-in you installed was somehow buggy and started adding no-follow to internal links. And even then, it wouldn't have been a penalty, it would have happened because you interfered with internal PageRank circulation.