I just installed the hyper 212+ and my cpu temperature in bios is 46 C. Not overclocked cpu. Is this normal? I may have messed up when applying the thermal paste, I didn't clean it off when I first took off the stock cooler, instead I applied more paste and spread it around, then it was left in the open air for about 5 hours. That is when I installed the hyper 212+. Would it be a good idea to remove the existing paste and reapply some? If so, would I have to remove my cpu from the socket before doing this?
High temps: it's summertime in the Northern Hemisphere. If your system is not in an air conditioned room, your temps are going to be higher. If you do not have good air flow through your case, even with a good cooler, your temps are going to be higher.
Alcohol won't do anything to the motherboard, but if it contains thermal compound it may cause issues. Remember you only need a little bit of thermal compound, the tube that came with the cooler can be used like 5 or 6 times easily. See how to properly spread the grease after application:
Note how little is used. It's really just there for the microscopic "holes" and "dents" in the CPU and heatsink, not to provide a layer for the cooler to float on.