Destroy Vindicator beams. Ignore the Hyksos, one of your wingmates usually lobs a bomb at it (IIRC). If the beams (or the Vindicator) is/are down once the Hyksos arrives, there's very little that can damage it.
After that, attack enemy ships in the order they've arrived (I dunno if some stay longer than others, but this usually works for me).
I generally go in an Ursa. Boa is a crappier bomber but it can hold more bombs in the lower two banks. Alternatively, get in a Persie and load it full of Stilettos, going after the Vindicator's beams and then the other ships' engines. You will likely have to reload several times so keep a support ship handy (as in, tell it to reload before you actually need it so it'll be right there when you do. This is a dick move to your wingmates but they're AIs so no one cares).
PS: Is there a FS2 Open 3.6.13 beta or just the nightly builds (if so, point me in right direction please) so far? I'd like to use that so I can try the latest furyAI.
SCP doesn't really do "beta", that would probably convolute the system too much. There's only the nightlies and Antipodes builds (for huge new features like the new pilot code). Nightlies are usually pretty stable though, and there are always epic new features in there.