Well since taking the case side off made your temps drop, it seems to indicate your case has poor airflow. A case with proper airflow can actually see increase in temps with the side panels off.
As for a fan, a fan is a fan, most computers use 80mm as a standard. Cutting slits would seem rather difficult, since to look good, they would have to be pretty straight. With the hole saw, you just drill the hole in your case, and screw a fan and grill on and you are done. The three inch spot you are talking about is for an 80mm fan. All the fans can be intake or exhaust, you just turn the fan around.
AS far as dust, its not really a big deal, you are going to get dust in there anyways, its smart to clean it out everynow and then anyways.
What AGP options are you looking for? I have not seen the FAQ, or what they are recommend? Just stuff like FastWrite, Aprature Size?
As far as the Artic cooler, do you plan on needing the PCI slots? I know having the option to is nice, however I haven't added a PCI card to my system in a long time, generally I subtract cards as the motherboards I buy keep making stuff on board.
Sounds like a little case modification is in order, and your temps will come back down.
Mainly you just need to get some fresh air into the case. You can leave the case open if you wish, you are correct the dust will build up a little faster, but nothing an air can can't fix.
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