Now it's done in single board form! Two SMA connectors are GPS antenna and frequency counter input, connecting to PD5 of ATmega328 through single gate inverter element. Rotary encoder change gate time for frequency measurement. Coin battery (CR1220) keeps setting of NEO6M (8MHz clock generation..). The RED toggle switch can select the connection between CP2102N to NEO6M or ATmega328, which enables GPS monitor or Arduino sketch upload through USB. As same as most of my board, onboard Lipo battery charger is prepared. The Yellow toggle switch change the clock source of ATmega328, on-board 8MHz crystal or GPS trained signal. Actually NEO6M generate 8MHz even before GPS locking (with low precision) and after GPS clock capturing, it goes to atomic clock precision!. 

Here is the measuring result of a clock (1 MHz) generated from another GPS module. As you see it surely measuring.. Yes, it's battery operation!!