Though I haven't tried such a fast run and it's been a while since I've played the REmake, here's some tips.
1. Use Jill Valentine.
She may be slightly weaker, but she's faster. She can also bypass certain locks with the lockpick, when Chris would have to hunt for keys.
2. Avoid enemies.
If you shoot zombies, you have to burn them within a certain timeframe. If you don't, they become Crimson Heads, which will chase after you. And the time it takes to kill them and burn the bodies is quite a bit, since you can only burn 2 at a time. The exceptions are bosses, like the Yawn and the Tyrant.
3. But, if you have to kill zombies, try to stack the bodies by killing them all in the same spot.
This will allow you to burn multiple zombies with a single portion of kerosine.
4. Run everywhere, even if it kills the atmosphere.
Except the puzzle with the crows. It's easier to take your time, since they won't attack you unless you run.
5. Make sure you know the solutions to the puzzles.
It will save time if you know it all in advance. But, since you've been trying for so long for a 3 hour run, I imagine it's redundant advice.