I have to agree with tiger. The completely free form build will lead to serious balance issues, because extremes tend to lead to real problems. I mean, imagine a force of 100 tiny ships all equipped with max strength lasers. They'd hit for 7d6+2 damage each, and you'd get 100 shots a turn with them. Or just do 7d6 but they each get 3 shots, giving you 300 shots a turn. Sure, they could be defeated by a ship that has 44+ armor, but barring that they'll annihilate anything even with the damage penalty for range. Then again, the largest ship has so many points, it could get 44 armor without a thought, along with 100 firing rate on its weapon and a couple hundred points worth of damage, while still leaving room for other stats if really desired, like 50 or so points of movement speed to get right next to people before unleashing its laser barrage (or missile or ballistic).
Actually, the original force isn't really a problem, because tiny ships are made completely worthless by any ship with an armor value of 44 or higher, smalls by a value of 50 or so, and even mediums are rendered near worthless by a ship with 70 or so armor, and that's only if the ship invests everything it has in damage. Looking it over it seems like fights will devolve into using nothing but the largest class of ship, because any smaller class can be made completely worthless by devoting a chunk of points to armor.
Oh, wait, ablative armor, so no, we're back to using 100 tiny ships to blast everything into non-existence. because they'll overcome any amount of armor that can be thrown at them. Sure a huge ship could have a 100 fire rate weapon and blast large swaths of them, but the fighters are likely to win.
Some ways to help alleviate these problems would be diminishing returns on stats, different values for different stats, and hard limits on stats.
Tiger pointed out the possibility of making speed more expensive for the larger ships, I think that makes sense. The small ships should be able to buy speed very cheaply, while the larger ships should be hard pressed to even reach double digits. You also may not want to make armor ablative, but make it very expensive, so that small ships would only have a point or two at best, while large ones might have 20 or so if they really want. Also, weapon damage and firing rate should be slightly more separated. For instance, instead of simply buying extra shots at the cost of a pittance of damage, make the ship buy multiple weapons, each of which gets one shot, and has to have damage paid for independently. This allows a huge battleship to have main guns along with some small weapons for picking off fighters without turning it into a death platform. Perhaps provide a bonus for only using one weapon type, or a penalty for having more than one to make people pay for a diversity of options on a ship and force their hands to make specialized ships.