^^ I think that is a good purchase, regardless whether it is a refurb or not. Usually some people including myself are against pre-built gaming systems, but in this case for the price of it (I'm assuming it was $750 something?), it is a good buy, since the i7 920 CPU and motherboard alone would cost $450, another $200 for the 9GB of DDR3, and $150 for the GTX 260 video card.
To answer your other questions, you might want to hold off opening the case until you actually turn it on, run some benchmark and stress test, look at the CPU and GPU temperatures. If you're unsatisfied with CPU temp (maybe it's 60C on load, which is a tad too hot), then go ahead and open it up and see what CPU fan they use. If it's a stock fan, you can replace the stock thermal paste with the arctic silver by removing the stock fan and wipe the old paste off with rubbing alcohol on a tissue, then apply the arctic silver. If you want to replace the fan altogether, see how much room you have for the CPU fan before purchasing one. Some CPU fans are ginormous and may not fit inside the case.
I'm certain that the wire connections inside the case are all fine. I mean you can double check, but it's unnecessary to take everything apart, unless you plan on transferring the parts to another case.