I started rebif, three years ago, and suffered similar symptoms.
My ms nurse, had got me to start on a 1/3 of the dose (rebif 22) by ejecting some onto a tissue before injecting.After a week increasing to half and then 3/4 before injecting the full dose after 2-3 weeks.
At first it was bareable, I had heard about headaches and flue like symptoms, and expected some. I was encouraged to take paracetemol on the night of injection and also on rising the next day if needed. Unfortunately for me it got worse as the dose went up and I never got beyond 3/4 of a normal injection dose. By this time I was taking the full dose of parcetemol you can take in a day, every day, and I still felt awfull.
A constant headache, awfull aches and pains etc, I really felt it was slowly killing me. After about six weeks I talked to my ms nurse and she suggested I stop and see how I was without (I think in case it was a relapse and not the rebif) and to go in and see her after a fortnight.
I think it is important to realise that many people get head aches and feel bad for a while at the start, but for the vast majority within a short time their bodies get used to it and symptoms reduce hugely. I do know a few people on rebif who always take paracetemol on the injection night and then are ok until the next time.
For me within a week of stopping rebif my headaches and other symptoms had dissapated to the extent that I no longer needed any paracetemol at all,( quite a drop from 2 every four hours) and within 10-14 days I felt okay again.
I started on copaxone a month later and have never looked back. For me few side effects and fortunately injection sites have not been a problem so far. Two and a half years so far.
There are two sides to every story, two of my friends have had to stop copaxone, one because it was not helping her relapses and the other because of injection site problems. So it is a matter of what suits an individual. Interestingly most people I know on rebif are on rebif22 I thought it was thought rebif44 gave very little extra benifit with a whole lot more side effects from the extra concentration. Ity seems that the consultants opinions vary around the country as a number of people on this site in England seem to be on rebif44.
I hope things improve for you soon but if they don't talk to your ms nurse, it is good for them to know you are in trouble.