As Chas' examples kind of highlight, if you want to keep the damage the same as it is in the current version, bring up the displacement tonnage of the spinals by 10x. Power by 10x as well.
Or
Keep as is, but then drop damage by 10x (so it's x100 not x1000) - functionally the same.
As for starting from scratch, as to what WBNC has said before (and many of us as well); if we were going to start from scratch:
1) Have 3 categories. Railgun, Meson, Particle.
2) Each category have a simple formulate based on spinal mount weight. Example:
Railgun Spinal: Medium Range. 1,000-50,000 weapon weight. 1DD (x200) per 1000 tons. 100 power per 1000 tons. Damage reduced by 1% per target's armour points. Cost 10MCr per 1000 tons.
Meson Spinal: Long Range. 1,000-50,000 weapon weight. 1DD (x200) per 1000 tons. 500 power per 1000 tons. Armour ignored. (Screens to function as per whatever screen rules). Cost 100MCr per 1000 tons.
Particle Spinal: Very Long Range. 1,000-50,000 weapon weight. 2DD (x200) per 1000 tons. 1500 power per 1000 tons. Damage reduced by 2% per target's armour points. Cost 50MCr per 1000 tons.
A DM -4 penalty to hit applies targets that are smaller than the weapon size. DM -8 penalty to hit targets smaller than (weapon size / 10)
TL table to still apply, granting up to 40% size reduction for example.
The above is a SWAG (scientific wild ass guess) btw - just a quick brainstorm around a simple solution. With a basic forumula in place, we can then tweak the actual values to make sure it is "balanced". Based on the above, a Particle Spinal that weighs 50,000 tons (or 30,000 tons after TL bonus), can potentially 1-shot a 300,000 ton ship. Thats a 10:1 to ratio - but it is completely unrealistic. It assumes max damage, a free floating spinal weapon with perhaps a saddle and a guy in a space-suit, and target with no armour. Realistically however, you end up with a 40,000ton battle rider, wielding the top-end particle spinal, 1-shotting a 136,500ton cruiser that has 12 armour, on an average damage roll. That I think is much much more palatable