Hi, this is my first post.

First off. Windows 7 USB connection to the GPS (no serial ports / modern
computer) and I'm pretty sure that is my main problem.

Past few months, I've been trying to figure out my timing issues. Lots
of reading & trying to figure out how to best configure everything. I'm
typically still off (randomly) by 20-100 miliseconds. I'd like to at
least get to within 50 microseconds (nanoseconds would be wonderful)

1) I need a computer with a serial port. The curent GPS module I'm using
is INTERNALLY RS232 --> USB converter, and recognized by my windows 7
computer as: "Prolific USB-to-Serial Comm Port (COM3)" ... the latency
and jitter is horrible, and both are seemingly random.

2) I need to run my stratum 1 clock (connected to the stratum 0 time
source via old-school RS232 serial) on linux or a form of BSD with
support for kernel timestamps, and a version of NTP with a driver to
supports my reference clock... points 1 and 2 seem fine.

3) I'm clueless about mounting an antenna, running cable, grounding /
lightning protection, etc... Really want an easy to install one.

For software, I've used 4.2.6 (stable / production) as well as 4.2.7
(dev version) NTP and haven't been able to tell any difference.
Just using the generic NMEA driver / this is a no-name cheapo SIRF module.

Also, trying to wrap my head around these:

http://linuxpps.org/wiki/index.php/LinuxPPS_installation
http://linuxpps.org/wiki/index.php/LinuxPPS_NTPD_support

And here is where I give up. As the subject line suggests:

HELP!!! I'd like to convert L1 GPS timing signal(s) into local time on
computer(s)

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