Visa Queries regarding overstaying

Hello . I am an international student from India on my Tier 4 student visa for my Master`s course.
My visa had expired on the 21st of April 2012 but my course end date was 30th of June 2012. I decided to extend my current student visa through the university international student services.
I decided to use my parents bank statements from India for this purpose however the courier company misplaced my documents that were required for filling of the visa because of which i wasn't able to send my application before or on the 21st of April 2012.
when i received my documents on the 23 i managed to file it on the same day through the university. i have received my bio metric letter from the UKBA and have got my finger prints done.
I wanted to see if some one can provide a satisfying reply to a few of my queries as i have spoken to many people including the UKBA and were not able to give me a satisfying answer
1. what are the consequences of this of late application?
2. what are the chances of it being refused ?
3. what are laws that i should follow so i don't get in trouble with the embassy regarding work ?
4. will this cause problems with my future applications ?
5. will it cause problems when i go back home ?
6. what should i do if it gets refused how many days do i have before i have to go back to my country

Please do reply as these thoughts have become a constant nightmares for me. Your reply or comments are greatly appreciated and i thank you for your help in advance.