This answer does not directly address the pin conflict issue, but rather skirts around it.
I have been looking into this same issue for over a month now and have come to the conclusion that the best option is to either purchase, for around $30:
or make, for around $20 (+$60 for the modules)
a shield that uses the SIM908. The SIM908 comes with both GPRS/GSM functionality, and GPS functionality, whereas the SIM900 only has GPRS/GSM. Now, there is no longer an issue with pin conflicts, as instead of two separate shields, only one is required.
The only disadvantage is that if you already have a GPRS/GSM shield, then that purchase will become redundant.
As an aside there is an alternative of a 3G (WCDMA and HSPA) and GPS, using both assisted-mobile (A-GPS) and mobile-based (S-GPS) modes, combined shield, from Cooking Hacks. A bit more pricey though, at $160.