Thanks for this post, I was on the same kind of questions. Do you know if it's possible and simple to do 3D kriging in Q-GIS? As far I know is not possible in Arcmap without buying an extra software as Target for GIS.
I am just curious about the state of this Python question. Any new? I need to learn a programming language and I was heisting with Matlab and Python, so if FEFLOW go into the python direction this would be a strong argument.
Have you some marly layers ? Or is all sand and gravel? Anyway even if you have marls, I agree with Gianmarc that 500 is a lot, base on what I read the ratio is more about 50-100. Perhaps could you increase your recharge?
I don't know if there is a simple manual... I think the only bottle neck is the interface which is not necessarily implemented in FEFLOW already ( not able to do unsaturated flow into PEST for example), but if you work only using ASCII file without the FEFLOW interface, you should be able to optimize any kind of model. You can download the PEST manual into the http://www.pesthomepage.org/Downloads.php.
Personally I did some test to see what is the effect of using multiple core for regional models (2 mo nodes). It seems that above 3 or 4 cores, the time-saving is very little. However if you plan to run several models at the same time as for PEST calibration, having multi-core is a really good improvements.