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Update:

I did fly back to my home country and landed yesterday @ pearson Intl Airport. CBSA gave me a very hard time questioning why I overstayed in Canada for such a long time and even threatened to cancel my PR. I had to explain everything and said I cleared my status by myself as soon as I got my PR visa. Eventually the guy let me land as PR
 
HI Matthew

Saw some recent posts from you and you seem really informative . I am currently in a situation, it would be very helpful if you can suggest me something. Thanks is advance.

I am from India and came into Canada as a student. I obtained a PGWP after studies which expired on 25 Sept 2014. The extension was denied for obvious reasons as we could not get a LMIA by then. So within the 90 days restoration period i have applied for a Restoration of status as Visitor on Dec 12 and still waiting for the reply from CIC on that. During the wait, my employer re-applied for Dual Intent LMIA and got an approval last week. My question now is, do i need to go back to India( as india is not a visa exempt country) and apply for work permit or is there any other option? Pretty confused about this

-Prashanth