Not 100% sure what you mean with 'fMRI timestamps' but since you say 'recording' I assume it's the TTL/optical trigger produced at the start of each volume? And since you mention windows 98 and < 10mSec the in-house software is maybe using the parallal port? From former experience with such software: that's usually a mess, especially on later versions of Windows where direct access to such port was being ruled out.

Anyway the principle is you use an A/D converter to digitize the signal then save it (either the complete signal or just timestamps of rising edge, the latter can also be done directly on some A/D cards). In the system I'm currently working on I'm using National Instruments PCI-X cards their C SDK to get the data but that's just because I need I/O channels for other things as well and because it has to include online processing of data. Otherwise you could just save the data at a nice and slow rate using Labview or Matlab or ... (pretty sure there are open source solutions as well). And there are many alternatives to National instruments as well of course. All woth resolution down to a couple of nanoseconds if needed. But note that it's still not trivial to get an accurate 'time of day' timestamp from it (should that be needed): at the recording site there's no way of knowing exactly when the data acquisition starts. And there can be clock drift.