1. Is it incorrect for the cooler fan to be blowing opposite the case fan even though they are only an inch apart? Seems to make more noise, and less airflow than just removing the case fan.
This is a totally wrong installation of the CPU cooler fan.
2. Should the fan on the cooler be blowing at maximum speed constantly? I thought it should be variable?
It's normal for the fan to be connected to the CPU PWM fan connector and temperature controlled variable fan speed enabled.
3. I also bought a front panel USB/memory card reader. They installed it by running the USB cable out of the back of the case, and plugging it in that way, rather than plugging into the motherboard. They did mention that the case is a very tight fit, but it would seem they could find room for one more wire on the motherboard.
This is variable depends on the options of the case and main board selections.
4. Would it be okay to replace the fan on the cooler with a Scythe slip stream? Or should I replace it with something else?
The fan that came with your CPU cooler will work great for you when properly installed.
I've had great experience with Directron in the past, so I don't really want to beat up on them over minutiae. But, I kind of feel like I should bring the computer back, and tell them to change this stuff, but I'm not sure if that's fair. What do you guys think?
By the time you go to all the trouble of taking the system back to them you might as well fix it yourself by changing the BIOS setting for fan control, except that the fan needs the blow direction changed. If you don't feel up to doing this yourself then talk to a manager at the shop. Please report back to us publicly about how this goes.