Hi,
This looks more like an integration task… with little to do with GPS.
Perhaps I am not the most qualified to answer.
I would say that for a standalone solution you need to control the weather station with a simple MCU (ARM7 or Cortex-M3 will do the job) which wakes up periodically to store the data on the flash card and then puts everything to sleep again. I could suggest a STM32F102 or a LPC134x to accomplish the task. The BOM should be around 80 USD including the GPS.
For a connected solution - if a simple cellular modem works - I would suggest to use something like a Telit GL865 or equivalent (Sparkfun has nice breakout boards). The module can be programmed with python to do the data collection and go to sleep again. Some cellular modems also embed GPS so you can save some money there, but anyway this case will have a BOM twice more expensive than the above.
Of course a proper answer needs a thorough requirements definition… I don’t think mine will bring you very far but I gave it a shot.
Best wishes and good luck with your project!
Michele