W4 witholdings for H1B-F1

I recently got married 15 days back and my tax situation is as follows. I was on a F1 visa till October 2015 after which my H1B visa kicked in. So I'll be a resident alien for tax purposes. My wife is on an F1 Visa hence treated as a non-resident alien for tax purposes. We plan to file our returns as "Married filing separately" since she will be treated as resident alien for tax purposes and subject to FICA withholdings if we file our returns jointly.The questions I have are as follows: 

1) My current deductions on W4 is 3.(A-1, B-1 and E-1 for head of household). Should I change my number of deductions to 2( only A & B) since I do not qualify for "Head of household" status anymore? 

2) Also in the W4 withholding certificate should I check the "Married" checkbox for "Married but withhold at higher single rate" box? 

3)Is filing as "Married filing separately" or filing jointly recommended despite the additional FICA witholdings?

Please advise on the above.