I was a grad student from India on F1 visa since July 2003. I graduated in December 2007 and was on OPT from January 2008 to September 2008. I changed to H1B on October 2008. Here are my questions:
1. Since I have been in US for more than 5 years as a student, I cannot use form 8843 to be treated as an exempt individual in the substantial presence test unless I attach a statement saying I do not intend to stay permanently in US. I cannot provide that statement since I plan to apply for Green Card by end of 2009. Because of this, I will be considered as a resident alien for tax purposes right?
2. If I am considered as a resident alien, will I have to pay the social security and medicare taxes for 2008? These were not withheld from my paychecks in 2008. Though my employer have started withholding these from my paychecks this year (2009), what should I do about 2008?
3. Should I use the SIMPLE IRA payments (Box 12 entry, code S, in W2) anywhere in tax calculations?

Thanks.

1. Yes, you are a resident alien for 2008.

2. Yes, you should have paid social security tax and medicare tax for 2008. I do not know the best way to pay it now.

3. Don't know.