Just a thought:
Are your case and power supply cooling fans working? Dusty innards inside the case?
Probably not your problem, but you never know.
I had issues early on with the game on my old rig of the game crashing about an hour or so into the game. I could usually set my clock by it.
I tried everything-more RAM, defrags, registry cleaning, different settings-nothing helped.
Then I read something on the forum about blowing the dust out of the case. It got me thinking and I checked my fans too-neither were running.
I blew out the dust from the case and ordered a new case fan and power supply. Until they arrived, I played with the case opened up and, lo and behold, no crashes.
The whole problem was a heat issue.
After installing the power supply and fan, I didn't have any problems.
Like others have said, it is more likely a mod issue or, like jimbuna said, SH3 just being tempermental.