Your query is answered as below:
Query 1
Due date for filing return of financial year 2008-09 was 31/7/2009 u/s 139(1). Beleted return u/s 139(4) should had to be filed upto 31/3/2010.
Any assessee whose gross total income exceeds maximum limit not chargeable to tax i.e. Rs.150000 in your case now it is Rs.160000, are compulsory required to file their return else they will be liable for penalty of Rs.5000/- u/s 271F.
Since in your case you were required to file return and you didn't filed till 31/3/2010 therefore you will be liable for penalty u/s 271F.
As I can see in your case that you were not required to pay any tax as tax payable was covered through TDS hence the AO may at his discretion waive penalty of Rs.5000/- u/s 271F.
You are not liable for interest u/s 234A as you don't have any tax dues.
Query 2
If any assessee fails to submits documentary proof to employer required for claiming deduction under chapter VI i.e. u/s 80C, 80D, etc. then he can claim deduction at the time of filing his return. So you can claim deduction when you file your return.
Query 3
Today everything have gone online and no documentary proof are required to be submitted with return of income
Hence you are not required to submit proof at the time of filing of return. But you should have these proofs in you hands because if any scrutiny comes u/s 143(3) then you should produce these documents before AO.
As far as HRA is concerned you have to make agreement for taking house on rent with your landlord and take rental receipts from landlord duly signed by him. Only then you can claim deduction under HRA.
Think that this will solve your query.