Fuel, you don't mention what you're trying to run, at what speeds, and in what type case, which might help suggestions and diagnoses.
However, a few things sprung to mind as suggestions:
If the GPU fan is standard orientation (on the PCI side of the card) having a correctly oriented fan _in_theory_ should not harm the performance of the gfx cooling. However you may get noise weirdness due to the GPU fan getting slightly overspun (perhaps) by the PCI fan. However, if you sort out your overall case temps then the standard cooling solution for most GPU's should cope with the load without alteration, providing you're not overclocking the card.
As Andrew says, thermal paste, decently applied, is a must. Remember as little paste as possible! A _thin_ layer across the contact patch is enough providing the heatsink's sorted properly. Too much goop actually impairs heat transfer.
As far as CPU sink is concerned, try and find the largest one you can generally, as these often come with larger/slower fans. The cooling potential is usually as good as or better than an OEM heatsink/fan combo, and will often have the benefit of running quieter. 60mm fans running over 5000rpm are a pain...
Casefan wisdom I've seen follows the premise of "heat rises upwards", so you want big and slow input fans in the lower portions of the case where all the cold air is. Again, a bigger fan running slowly is often better in terms of air transfer and noise than a small one frantically spinning.
I've always regarded case extractor fans as optional - you already have one fan pulling air out of the system in the PSU normally, and to assist this and prevent dust problems you ideally want "positive pressure" in the case.
What this means is you have more air actively being pulled into the case than you have being actively pulled out. This ensures that dust doesn't get drawn into your system through convenient apertures like the CD-ROM drive, for example. A problem you don't really want to have...
Try these things step by step, I suggest. Start with the thermal compound, and see if that helps. Then I'd say go for a larger CPU fan, then a large single casefan drawing air in wherever you can fit it. You may find with a decent CPU cooler you can stop the process there.
Good luck, and try not to do what a mate of mine did and progress to spending hundreds of dollars on watercooling.

Happy trails.