Well a small help is if you an find a MAC compatible upgraded CUDA GPU that will give you hardware MPE acceleration in Premiere to install in these units. Not knowing Mac very well I cannot give you specific models. Your 2009 unit has a antique CUDA GT 120 but with only 512 MB of video RAM. You need 1 GB or more of video RAM.
What about the graphic card?
What would you suggest to do for the setup to maximize it´s potential (For now it´s working fine)? Would it be good idea ome 7200rpm hard-drives for media and cache storage or do I need that or can I see significant improvements over it since there is still 3 3,5" internal hard drive bays with SATA II connections (and the two eSATA ports).
First and foremost: keep an eye on that 480G PCI-E SSD that you dumped a lot of money into. Those OWC drives aren't known for their robustness or reliability (OWC folks will argue with that statement. Ignore them). Since OS and apps are easy to re-install, it may not be a big deal. But don't put any of your projects on it, even though it's a fairly quick device.
Second, start adding SATA drives to the other 3 bays. Fill them up with the biggest drives you feel comfortable buying. Make one of them a 10k RPM drive for your scratch space. The others can be 7200RPM drives; since you're limited to SATA2, there's not much use in trying to crank serious disk bandwidth through the system.
Video cards. Get rid of those OEM garbage cards. Drop them into a chipper/shredder, in fact. Contact this guy about getting flashed nVidia cards that will work in both Macs, and will help with Pr and Ae. Dave can sell you a flashed GTX780 that will boot (with grey Apple screen) and run in the Mac just fine. And it'll outperform anything Apple has ever sold for those Mac Pros.
Jason, thanks for filling in the details, I do not think I have ever even seen a MacPro up close so I am no good with any details. I did build a Hackintosh a few years ago but that is a far as I have gone.