Keywords not ranking for homepage not in google

I was hit by a manual penalty 6 months back and cleared everything, However after all that happened I started making links again but I don't see my keywords in google linking to my home page however there are few keywords on 3-4 page ranking for internal page which has no related content whatsoever. Can anyone please help me understand this situation?

Has the manual penalty been lifted?
You have not mentioned this vital fact

lucasbraydon said:

Has the manual penalty been lifted?
You have not mentioned this vital fact

Click to expand...

Yes, it was lifted.

hotantivirus said:

Yes, it was lifted.

Click to expand...

What was your link status after you cleared the penalty?
What is your competition for the keywords like?

That aside, I found Google take a further 3 months minimum before they allow a site to re-rank strongly for a phrase it was previously penalized for.
It's quite common for inner pages to rank in that time. A PITA I know.

Also - look up "Rank Transition" which Google brought out about 2 years ago. While not officially implements, it's a method they use to DELIBERATELY feck about with you to see if you over-react. It is known that this algorithm extension is aimed at examining the reaction of webmasters to "bouncing" and lower than expected results (or even higher) to see if they resort to spamming links as a response (among other things) Watch out for this and don't be tempted to be aggressive. It doesn't work.
In any other form of punitive realm this would be called entrapment - but Google don't give a fuck about mortals or ethics.

http://www.demondemon.com/2012/09/15/google-transition-ranking-and-extreme-index-changes/

Scritty