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You DO NOT need to go for VISA stamping as its valid until 2011. You seem to be on-status all along, and your VISA is valid until 2011.
Here is what you need to do,
1. Transfer your SEVIS information : After you get acceptance letter from the new school for your PhD, they won't issue you an I-20 until you ask your former school to transfer your SEVIS information. So you need to transfer your SEVIS information to get your new-I-20 issued
2. Expiration of OPT: Regardless of your OPT expiration date on the EAD card, as soon your former school releases your SEVIS information, the OPT expires immediately. So in your case, you plan to leave for NEPAL in April 09, you should have made the new school issue the new I-20
3. Validation of new I-20: Until you sign the new I-20, its not valid. So, as soon you get the I-20, sign it and send one copy to school and other copy to yourself( they will send you two copies, one for their record and other for yourself, or you can make a copy, keep yourself the original, and the copied to the school)
4. Signing the new I-20 by the new school's international student advisor: Before you leave for Nepal, you need to make the new school's international advisor sign I-20 at the third page, which basically is the permission to re-enter the country and attend the same schoo after a temporary absence from the USA within a year of the date that the registar signs that form.
Cosultation: As soon you receive the new I-20, you need to consult with the new international studnet advisor about your travel plan to home, so that they sign your I-20. Also, make sure that you carry all your I-20's, orginal copies and EAD card along with your passport and Social Security card when travelling.
As long as you have valid VISA, you don't have to worry about re-entering, unless you have come criminal record in USA. I had three I-20's from three different schools with me ( travelled in summer 2006, VISA expiration date was December 2007)
Disclaimer : This is my personal experience, please do your best judgement.