(BTW, it looks like actlabs lightguns work pretty much the same as the arcade games. The major difference is the box that gets plugged in the video output. So look at how the actlab guns work for more details.)
ok. so the optical signal is timed based on which pixel it is pointing at. The data file seems kind of vague. I would assume that the gun's PCB can sense the refresh rate(if not where does it get the sync?).
Easy for the arcade gun: from seeing the screen being drawn.
When the optical sensor sees the up-spike of brightness of the beam drawing the new line, it sends the signal. (Since a white screen has the biggest spike, it's the easiest for the gun to see, so that's why happs suggests the arcade draw the screen white at trigger pull: for a more reliable seeing of the spike.)
It's the arcade PCB that needs to know the frequency to calculate the location. And since it's the source of the video signal, it knows the frequency.
But per my understanding of this I conclude it would require:
A PCB to decode the tracking info and accept trigger signals. the board would receive the trigger, optionally flash the screen, then pass the tracking info on to the computer as a mouse click at the co-ordinates. I guess it could also have an adjustable auto repeat interval until the trigger debounces(but that wouldn't be in the first prototype).
My understanding is still lacking on the timing of the optical signal. I would probably have to buy one to mess with it. But I still run into the problem of not having any data analysis tools at my disposal. If I had defined specs, I could probably design a circuit for it, but that seems like it might be impossible unless we could convince someone to "take one for the team" and buy one to analyze it. That would be a lot to ask of relative strangers. Any takers though?
Would I be right in the assumption that the data rate on all standard Pc buses would be too slow to write an acurate virtual waveform analyzer for a computer? Cause if it is possible, I would personally offer to waste my time to try to hack one together.
I guess I could try to talk to Happ to get some more specific answers about their output signals. Are the tech support ppl that knowlegable anyway?
If I made a device it would probably be a serial interface so I hopefully wouldn't have to use eeproms -- might not be able to avoid this 
I will try to post updates to the situation, I was hoping this would have any easy solution.
Since the actlab and the arcade guns work so similarly, with the black box that comes with actlabs guns doing what the arcade boards did, I'd suggest checking out what's in the black box that comes with the actlabs gun.
AFAIK, that black box:
a) gets the vertical and horizontal refresh rates from the video signal (and probably calibration, too)
b) intersepts the video signal and sends a pure, too bright, white signal starting from the next new screen after the trigger is pulled
c) takes the time it takes from the start of the new screen until the optical signal from the gun comes and
d) calculates the location
e) using the values from the calibration
f) and sends it USB mouse style to the computer.
That's all the board you're trying to make needs to do, except for arcade level results, you want to calculate the location even if the trigger isn't pulled (ie: add real time tracking).
Might be easier to hack a console gun to work on a pc. Do they have better accuracy than act labs guns?
Other way around. The actlab guns have the highest accuracy* of consumer lightguns, ATM. If an HD TV lightgun comes out, then the actlabs might have competion.
*(Assuming you calibrate the actlab gun correctly, and the video exactly fills the screen.)
Actlabs might have a higher accuracy than the arcade guns, too. Due to that the actlabs can work at
150 Hz refresh rate, while arcade monitors run at ~32 Hz, plus the higher resolution of PCs than arcades, it easily has a higher precision. Whether the higher precision comes out as higher accuracy needs to be tested.