Same case is with me, But I landed here on 25th Nov 2006. See if my comments helps as I was also searching answers of all these questions:-
1. Logically you should filled up 1040 NR b,caz in year 2006 your stay was less then 180 days. But It also depend on W2/salary slips entries too if your your employer already deducted helth/dbl eth then you have to inform about all these details to IRS so 1040 EZ (Mrried filling jointly ) should be ok in this case. In case of resident aliean you will get more tax benefits.
In case Non resident, India is a treaty country so you also get benefits there too. What benefits you will get that You have to ask some tax consultant.
2. I don't think you need to mentioned your inidan salary if you are filling 1040EZ.
3. You shoudl be ok by filling 1040 EZ(married filling jointly).
4. Your type of form will be totally based on your W2 columns/entries. If you go to any tax consultant, they will use your W2 entries in to their s/w and s/w will automatically picked up the right type of form.
Hope it helps.