How can i set a custom waypoint in CF 2.0

The JH you're searching is inside that big rock there...

Not sure if I understand your question concerning "custom waypoints" correctly(?) You can click everywhere on the map and set a waypoint (or best path) to that point.

Edit: Ah - didn't know that it's impossible on active missions.. thx Martin for the insight!

There is not possible set own waypoints during active mission (not even vanilla campaign missions allows this). You need use planets and suns in these search missions .. but, ... when you will go from triangulum on trade-lane, use turret view and look to the right. You cant miss it

Being unable to set waypoints during a mission has finally led to me searching through the entire Dublin system for a data disk, square by square, top to bottom, for a looong time in real time...and I still can't find it. I don't recall having this much trouble in 1.9, and the Dublin System seems rather different in 2.0. I had much less trouble with the other disks.

I don't think I missed any nooks and crannies, but I seem to be pretty well stuck. It's beautiful--like the rest of 2.0 so far--but I'm beginning to feel as if I'd like to leave
Dublin behind and get on with the story. I hope I haven't somehow glitched myself, but I'm beginning to worry.

Trent is currently checking under chairs in the Hood's bar, drinking to fuel another search attempt.

Got it, thanks! The waypoint didn't show up even though I flew past it twice.
I closed and restarted CF, and it worked fine.
Appreciate the help!