I have edited my post with a less annoying version of CotSC, as the parts now rotate slower (they are closer together), there are now eight fewer homing lasers (the only four are on the large rotating sections (the ones with beam cannons)), and the core is 30,000 hit points weaker. It used to be 80,000. Now, it should be MUCH faster to kill if you blow up all the sections. The problem you may have had is that you didn't destroy the four smaller quad-gun rotating things. They house repair boxes, doubling the effective hit points of the core. Even with the original 80,000 hit points on the core, it took me just a minute to blow it up when everything else was dead. It's also worth it to kill the rotating sections, as each of them spawns a goody. That's eight goodies you get before the boss is dead. When it dies, you get TWO from the main core. Comes to show just how difficult it is.
What should I attempt to create next? Possibly a Deimos-class corvette...
P.S. Your larger ship has way too many homing lasers firing at once. Make them fire quickly one-by-one, rather than all 20 at once, so that you actually have a chance to survive a wave.