Change the engine max_force values.
If you haven't already, extract data/equipment/engine_equip.ini and find the engine(s) you want to make faster. You should see a line max_force = 48000. To increase the speed, incrase this force. To decrease it, do likewise.

To determine the force you should use for a particular speed, multiply the speed (v) by the linear drag value for the ship+engine (600 by default). So, if you wanted to go v = 100m/s, you would need to use a force of 100*600 = 60000.

Alternatively, you could edit the linear_drag value of the engine. Most (all?) of the ships have a linear drag of 1, and the engines are 599 by default. Doing this, however, also changes how the ship handles.

For any other info, I suggest you use the "Search Forums" option above.