How did you made 3k km/s missile on MAGNETO PLASMA drive techs ?? That is like Nuclear Thermal level and even that is slow....
To add one thing coming from experience : Specialize.
Drop those buoy's, hangars, boarding craft and fighters, cryo berths, fighter crew berths, half of CIWS's ( 11 CIWS on one ships i a "little" overkill ) and you will gain some tonnage for more launchers and beam weapons.
I actually like the range and huge amount of armour - i think it fits the design of the massive capital ship that is meant to sterlize enemy planets and breach JP's and operate on long distances.