I know you refer to the Lively as the basis, but the broadly similar Leda class has a bit more information available... and she is a 1091 tun BM ship, displacing only around 1496 ton.
2000 is closer to the displacement of the much larger US superfrigates such as President/Constitution - 1576BM, 2200 tons.
Thanks for noticing this. I looked in the editor, and the mass of the ship is 1923 tons. 1800 tons of this is the hull (the guns are 90). It looks like this 1800 figure is one I wrote in by hand, rather than calculated, and I don't remember where I got it from.
I can see the relation displacement = about 1.5*burthen in a few places. I have one source, "The Command of the Ocean" by N A M Rodger, on the 18th century royal navy, that says "for a fully stored warship" the displacement is about twice the burthen. Do you know what the state of storage is for your figures?
This is something I am reluctant to mess with, as I am happy with the way the acceleration, stability etc. are tuned at the moment. But I will have to look at this stuff again if I ever get around to flooding and sinking.
I looked at the shot damage code (possibly for the first time since 2014). I'm tracking the kinetic energy of a shot. According to a comment in the code, an 18 pounder shot at 500m/s penetrates 2ft of oak, and I call it a hulling if the energy is more than that (with some randomness). For damage to crew and rigging etc. I just came up with some numbers that seemed reasonable, which shouldn't be hard to tune.
I set the rate of fire at the maximum plausible one. I agree it's a touch high. It would be good to model this better, and change it over time with crew strength and morale etc. Some of the code for this is there already but I'm afraid I'm unlikely to get around to fixing this up.
(And sorry, it looks like the 9 lbers are actually firing 18lber shot.)