I do not think flu shots will assist you. They are a vaccine, which should only help your defences from catching the flu.
A flu is a major trigger for a relapse for me. I spoke with my doctor, and he said that the split between bacterial and viral would be around 10-90 (ie 90% chance its viral). Antibacterials then would not be of much use in 90% of cases.
I now take Amantadine at the very hint of a sniffly nose as almost a profalactic, or if someone with a flu looks at me wrong; or sneeze near me in the train. If I am fairly sure I have caught something, I will start a 7 day course of Tamiflu. This REALLY reduces the flu if I catch it early enough. Anti-Virals do not actually kill the virus, but try to stop them replicating out of control. Tamiflu is a wonder drug for me. Cut back the flu & I cut back the severity of the relapse. Also, because I get over the flu quicker, its safer to start on the steroids which would of let the virus really run wild.
So the long and the short of it. If you can catch it early, Tamiflu is brilliant. Amantadine is cheaper, but I do not think as effective. Reading on Wiki, it implies they both should be ineffective, but that's not what I have found.
I actually got a flu while on rebif, and had my worst relapse ever, while on rebif. I did not see the anti-viral effects of rebif, unless this was one of the 10 out of 100 cases of a bacterial infection.
Hope u get better soon.