One trick that may work if internally consistent with your FTL system... 'warp' a projectile at a ship. Rail gun + warp port = rail gun speeds, but it appears 1m off the enemy's hull. Whammo. Warp torpedo on the 'cheap'... make a warp 'tube' from the rail gun to the exit point, and slam that puppy down it. No internal engine sustaining the effect. More like a wormhole, really.
Speaking of, wormhole + kinetic load/particle beam/laser = FTL weapon.
Hmm. Actually, if you can do micro-wormholes for communication, then...
Disperse a sensor net around your ship, synced to ship movement. Have it some insane distance out, like 100Mm. Little tiny autonomic sensors that use FTL communications (I'm assuming you have that) back to the ship to alert it of incoming energy weapons at light speed, or sub-light weaponry. You could have a secondary grid of defensive weapons at say 1km out that would then react to the data from the sensor net.
And this, folks, is why you want the geeks on *your* side.