1) Yes, that is correct. On 31 Dec 07, you had NOT YET met the Substantial Presence Test, so you should have filed either Form 1040NR or 1040NR-EZ plus Form 8843 one last time.
2) That is the typical IRS response when you file as a resident alien, then apply for the FICA tax refund.
You first need to amend your 2007 tax return, attaching a properly-prepared Form 1040NR-EZ and Form 8843 to Form 1040X and specifically request that they reinstate your non-resident alien status for 2007.
Once the amendment is processed, then you can re-submit Forms 843 and 8312 to request the refund of the FICA taxes.
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