here are my answers........I am not a legal expert; But these are based on my experineces and other people's experinecs..
1. My passport is expiring on November 3rd 2013. If I file for H1B coming April, can I renew my passport after filing my H1B in April/May or can I renew my passport now?
-- Usually u renew your passport when you have 6 months left. Just to be safe, before 3 months is considered fine. 3-6 months time frame is perfect. My suggestion - file H1B and renew ur passport when you have 5 months left.
2. When will my new H1B 1-94 expire, will it expire on November 3, 2013?
-- there is no connection between ur passport and I-94. I-94 is what governs ur status in US. You can still stay in US with valid i-94 and expired passport. However, not a good idea to have ur passport expired.
Ur H1B starts from Oct 2013, and usually expires in 3 years. So basically ur new I-94 will expire in Sep 2016. U might have few extra days.
But I have seen few recent H1B with just one year of I-94 so basically they got one year of h1b.
3. Do I need to leave US and go to Canada/Mexico or Nepal to stamp my passport on or before November 2013?
-- No. The only time u will need to stamp with h1b visa is if u leave US and need to re-enter. Unless u dont leave US, no need of stamping. Last time I checked, the first stamping has to be done in home country (not 100% sure on this; or may be this is just for other nationals).
But stamping at home country is usually encouraged.
4. Can I renew my passport after filing H1B? If I file for new passport, I will get it in 3 months i.e. April end. Can I update USCIS after I file for passport renewal?
-- Yes you can renew passport after filing H1B.
My suggestion - do not file for new passport right now, its very early.
I dont think you have to update ur passport with USCIS, either u will get ur H1b results way in before u file for new passport OR there is no connection at that point between ur new passport and pending USCIS application. But check on this one. Rules might have changed.
Side nOtes :- All new passport are MRP (Machine Readable passport). Heard that it usaully takes more time for MRP becuase they verify lots of infomartion. Contact Nepalese embassy in DC.
Hope this helps........