Viruses aren't exactly my area of expertise but let's see if I can point you in the right direction.
First, you need to do some basic flu research. Try googling something like "flu virus biology" for a start.
1. Check out the picture of the flu on http://micro.magnet.fsu.edu/cells/virus ... virus.html
When different viruses are referred to by H and N, it means the two proteins that stick off the flu surface, hemaglutinin and neuroamidase (not sure if I spelled those right!) The flu is always evolving new H and N proteins, that's why it's so hard to design a vaccine--it's a moving target--and why you can get the flu more than once.
2. I think you're on the right track--do some research on how vaccines are produced and how they actually kill it. A big part of what the vaccine scientists do is try to guess what kind of flu will be the big one to worry about in any given year.
3. I googled "immunology" and this was one of the first hits, looks like it might be a nice introduction:
http://www.biology.arizona.edu/immunolo ... ology.html
4. I am not sure about this, but your logic makes sense.
5. I found definitions here:
http://www.ncbi.nlm.nih.gov/Web/Newsltr ... LView.html
Here is what I THINK they're trying to say--If you get a hit that something matches, it means there were sections of the sequence that matched. Max is the score for the best-matching section, and total is the overall score for all the sections.
You have chosen a really challenging topic, and it's going to take some research to get up to speed. But, it's a very hot topic so I think with some searching you'll find some info on the flu and vaccines. Good luck.