Stock Heatsink installation

I don't quite think it's possible to put on upside down. Are you saying that when you were done the heat sink contact point (notable by the thermal pad on this side) was pointing towards you and not the CPU or are you saying a label / sticker was up side down when you looked at it ? The latter shouldn't matter.

As long as a) the pad wasn't damaged or malformed and you didn't bend the CPU by trying to clamp down hard on it w/ metal fins you should be fine.

Well the intel logo was upside down so I kinda thought it was upside down. And in the manual it was facing the other way then I put it so I kinda thought it was upside down.

Since I havent used it all should I have any problems with the thermal paste on the stock heat sink. I turned on the pc for a several minutes without the ram to see if it was transfering heat properly and the metal heatsink was warmer then when the PC was off (not to much warmer but you could feel it). I thought it shouldnt matter, but I am more worried about the thermal paste.

You're probably fine. When you get the system put together run Prime95 to put it under a full load and use a program like HWMonitor make sure the core temperatures don't go above 70-73C or so.

Yeah you cant really put it on upside down, its all the same every way. But you should be alright.