Ok I'm currently running an AAR for a small universe inspired by this thread, there are 2 NPRs and 12 systems, each starting empire's home system is connected to a lone system, that system is then connected to a third system which connects to one of the other empires second system, that third system then connects to a fourth system which has links to both other fourth systems, creating a complex symmetrical web of interconnected systems, making opportunity for many bottlenecks, salients, and back door invasions, sadly however after entering the jump points and editing them those systems are now visible to me, the jump points are visible also, I can however set the jump points to unexplored, so even though I can see the jump points, I'll hVe to consciously ignore them until the grav surveys are complete.
One tip for manually opening and modifying jump points, after setting a jump point to another system, sometimes the label for thatpoint will still say 'unexplored', you need to enter it so it lists the correct system, otherwise you may get confused. Good luck.