OK, so you did describe the fan direction correctly the first time. I've never seen such an airflow design, and you are creating considerable turbulence inside the case.
If I were you, I'd change to a much more STANDARD air flow, and not depend on your two poorly placed, smallest fans and seams in the case to get air OUT of the case.
Reverse the top fan and the rear panel fan. This will insure most air comes in from the side (large fan), and is drawn up to the cpu by the top and rear EXHAUST fans, some of which will be blown past your cpu cooler by that fan before exiting.
I'm not too worried about your small side fan being set to exhaust once the other changes are made. Although I would ask you to simply TURN IT OFF while you test the changes above.
After you test this suggestion, you can turn it back on and re-check cpu and vid card temps. I'll bet the cpu is worse.
THEN try turning off the LARGE side fan, and setting the SMALL side fan to in. I'll bet everything is cooler.