http://esr.ibiblio.org/?p=4171
Basically I’m suggesting taking the Skytraq Venus 628 you already have, populating the power backup, adding an ATtiny4313 wiht header and high-baud friendly crystal, a serial to USB and 5v to 3.3v, and some headers and things so it would be generic but the AT4313 could intersperse the PPS indication inside the GPS traffic. And it could be used for other things if the AT4313 pins were broken out.
Edit - I’m thinking 4313 for cost, but you could make this an Arduino or the USB-onchip variant ATmega328 level chip with the GPS attached.