These aliens are tough nuts to crack. I turned on my AMM sensors v2 and I uncovered 9 or so enemy ships firing missiles at me. Still can't be them, why can't it be something easy, like theoretical physics?!
Just do what I do: Build cruisers with enough PD, armor, and shields to absorb any size of missile barrage (short of A Certain Race armed with A Certain EW/Missile Cross), put together a decent sized squadron, and let them empty their magazines while you close. Once you get in range, open up with your PD and sandpaper them to death. You don't need missiles, and you don't need heavy EW. Just a crapload of 10cm quad lasers.
For an example of how this works: I had a squadron of 6 low-tech (around near-UV lasers, ion engines, etc.) Light Cruisers following this design philosophy absorb more than 1200 missiles, in volleys of 99, with serious damage to one ship, and medium damage to another. The four remaining at full speed caught up with the enemy ships as they were rearming at their base and shredded them with their PD at knife range. This will get you through pretty much any sort of Precursor or low-medium tech NPR force if you scale it up appropriately, with the added benefit of saving on missile and ship replacement costs. It also helps if you name the ships "Juggernaught 1 through 1+n".
Out of curiosity, why are pretty much all combat ships at least R3? Even tiny 1k ton FACs with a single weapon. It makes it near-impossible to put officers on every ship without SM promoting a ton of them.