Vast improvement (as in total 180 degree change). Kudos!
A few issues/concerns/questions:
1) What is the login section for?
2) Contact form: I see you are using jquery. Why not go ahead and use a jquery form? I think it is bad architecture to take ppl filling out the form to a white page with a layout that is not consistent with the main site.
3) Get rid of the Naija flag animation - I find it distracting
4) Animation on home page - IMHO, this is the site for the embassy in rome. If true, I think you should put a photo of the embassy. That animation you have there should perhaps go under "about Nigeria"
5) News Links: Is this going to be updated regularly? If so, are the necessary people trained to know what to do, or are you paid to do it? If the latter, even better. If not, I would take it off. I hate seeing stale news

6) I was once approached to redo the website for the Embassy in New York. One issue I raised was that it would be nice for all Nigerian embassies to run off a subdomain (e.g. rome.nigerianembassy.gov.ng or whatver) and that for uniformity (ala the US model), all subdomains would look alike, only differing in content. I am wondering if you could see to pulling similar strings over there. I didn't get the job but if I do, 3 things I would push for, for sure are the use of a CMS, sub-domains (at least for the US embassies/consulates) and a uniform layout. 'Something to think about.
Overall, this site reminds me of a song that was sang during the opening of a popular game show on NTA, back in the day, "I am proud to be a Nigeriaaaaaan"

Good job! I just hope the clients have appreciated the effort in cash and kind.