I was in a similar situation. Started on Copaxone & was on it for nine months. I turned out to be a non-optimal responder as well as suffering from severe hives at the injection site. I've been on Rebif now for almost three years. I can't recall exactly how long it took for my body to adjust, but I had the dreaded flu-like symptoms early on. Several things that may help you out. Staying well hydrated is crucial. Secondly, an earlier injection time may help as well. I was having problems with "wiftiness" and feeling like I were hit by a Mack truck the next day when I did it at night. It sounds counter-intuitive, but an MS Lifelines nurse explained that our metabolism slows down when we sleep and we can't stay hydrated during that time.
As for the Ibuprofen, I wouldn't worry too much about the dosage, save probably taking 800 mg is more than plenty. I take two tabs (400 mg) about an hour before the injection and then an additional tab (200 mg) a 1/2 hour before. It depends on where the injection is. You may also have to take more later on depending on how you feel. If you're concerned about the dosage, you can have your liver enzymes tested with blood work. I have mine done every six months or so and haven't had any problems. Yeah, more needles... Hope you feel better!