Matt, as for the extra fans, well you can always mount them on the side(not on the mobo side that is useless) and top expetially if you cut the holes your self, and you seem like a do-it-your-self-er.
Smaller cases arent neccisarilly bad, expetially if you have a few fans. It will actually have increased air movement because of less volume in the case, even though the air flow(CFM) is still the same. For those that are reading this and might not readily understand let me simplyfy the concept a little for you. lets say you have a 20" box fan. This fan will moce the same cubic feet per minute(CFM) whether it is in a 4'x6' bathroom or a 15'x20' living room, but the bathroom will feel more like a windtunnell than the slight breeze you would feel in the living room.
One other thing to keep in mind about case fans is to install them so the air flow moves in the same direction, kind of like a twin prop plane with a prop in front and one in back. The front prop pulls and the rear prop pushes. Also the power supply(P/S) fan needs to be taken into consideration. You dont want all your other fans forcing air into the P/S at the same time that the P/S fan is trying to force air into it, all that will do is make the P/S fan work twice as hard and there for wear it out quicker. Hope this helped explain it a little more.