Switching from EEA residence card to Tier2 Visa

I was a non EU family member of an EEA national for 5 years. I applied for ILR a week before the expiration of the 5 year leave but my application was recently refused last December because my EEA sponsor declined to back my application. I had to apply anyway (as a last resort) on account of my job which luckily is on the UKBA shortage occupation list (SOL).

The refusal letter states that though my EEA residence card had expired, they had considered my circumstance and that I am not required to leave the UK as a result of that decision. It neither says that I am allowed to stay nor continue to work. It is quite ambiguous. To be on the right side of the law, I immediately alerted my employers to try and regularise my stay through a work permit. They consequently obtained a certificate of sponsorship (CoS) for me under Tier 2 (General) which is valid till April 2014. I am now about to apply for the work permit;

My questions are;

(1) Will home office allow the switch to Tier 2 from my last granted leave of a family member of an EEA national much as they state 'You are not required to leave the United Kingdom as a result of this decision?

(2) Will the public enquiry offices (PEOs) entertain a same day service for such an application?

Please help.