1) Your temperatures are fine. A gpu will run hot, but they are built to do so. <95c is ok.
35c under load is good vor a cpu. If they get too hot, they will slow/shut down to protect themselves.
2) The case is not bad, but I don't think I like side fans much. They disrupt the natural flow of a case.
3) If you want to replace the case, look at the Antex 300 illusion model for $70:http://www.newegg.com/Product/Product.aspx?Item=N82E16811129066
Two intake 120mm fans with filters, and plenty of exhaust.
4) Any aftermarket cpu cooler with a 120mm fan will be better than stock. Your cpu will run cooler and quieter.
CM hiper212 is a good value. There are others.