Well, Minecraft can run on a potato so that's not a very helpful indicator. LOL.
So what CPU cooler did you get? And just for the sake of surety, I would double check all those case fans and make certain that the fan blades are facing out on the intakes, blowing in, and that they are facing in on the exhaust fans, blowing out. Easy to accidentally place fans incorrectly. Easy to check to verify that they are not wrong. I'm sure you are right, but always good to double check.
As far as "mounted to the top incorrectly", what, exactly, does that mean? Pictures would be helpful.
With that many fans, if they are correctly mounted, and if you have a CPU cooler that IS capable of handling the TDP of your processor, there are few other...