Routing traces for GPS antenna input
GPS (or any radio) RF trace to the antenna should not go across the whole board  because of the interference, as it appears in your design.
Some common sense suggestions are:


Place the gps chip to the antenna connector as close as possible to shorten the route. 
Avoid placing other components and even other traces near the antenna trace, this includes the other side of the board.
Make sure the impedance of the route matches the requirements for the chip and the design (for example, 50ohms). This depends on the material and thickness of the board and width of the trace. There are trace impedance calculators online, for example, the calculator at eeweb.com


In my opinion you should either use the SparkFun board that is properly tuned and tested, or transfer it completely, including the connector, and choose a PCB material that is similar if not exactly like the SparkFun board.