Q3:Depend on his qualification

of tax treaty (per article 19), if:
A) He can claim tax treaty, you couple are no need to file joint return---he files 1040 and claims his treaty; you files your 1040NR.
B) He cannot claim tax treaty, you can elect to be treat as a RA, and file joint return with him since he is RA in 2003 and you are married then. Doing so you can claim two personal exemptions, family standard deduction, and if you and your F1 University is eligible, you can claim education credits (IRS pub970).