BK, your hull costs should be relative to the general cost of the standard hull costs. Your basic hulls are the FF, DD, CL(?), CA, BB and DN. Most other hulls are usually based off of these basic hulls. Most CL classes are support ships containing a little more firepower than a DD, but also doing a fleet support function. So if you base the cost of all other ships based off of the basic hulls, you can get a better idea of what a ship hull should cost.
FF-260
DD-300
CL-420
CA-500
BB-800
DN-1000
A good example would be the ST's "Defiant" class. It is the only ship built by the Feds as a "Warship" and would be a special hull. It is basically a Destroyer Escort with the fire power of a Cruiser. Based on your costs I would price it between ~380-425. Now you give the player choices about building a CL or DD vs a "Defiant" type ship.
A ships ability to "take" damage and its weapons abilities (this will vary on type and sizes of weapons) are the key factors in pricing.
Hope this helps...