Wormholes Save Paint a Galaxy
A wormhole pair links two systems. In a save you can move each end inside its system, and add or remove pairs.
Move a wormhole
In a save, the system view shows each wormhole as a blue swirl where it sits in the system. With Names on, its name plate shows under it. Point at it to see which system is on the other side. Drag a natural wormhole to move it. Hold Shift to snap the angle to 15° steps. Shroud tunnels show too, but they stay where they are. Turn off Bypasses to hide them.
Click a wormhole, or its row under Bypasses on the system's page, to open its page in the Inspector. The page links to the system on the other side, and you can type a new distance and angle there. The selected wormhole has a ring around it in the system view.
Add a wormhole pair
In a Stellaris 4.x save, you can add a wormhole pair. Select two systems, right-click one and select "Link as wormhole pair". The Inspector's Hyperlanes section has the same action in its Wormholes block. Each end starts near the inner edge of its system, where the game puts the wormholes it spawns, so drag it where you want it. The option only shows when neither system already has a wormhole or shroud tunnel.
Remove a wormhole pair
To remove a pair, select the two linked systems on the map, right-click one and select "Unlink wormhole pair". This works on the wormholes the game made as well as the ones you added. A system you added can't be deleted while it has a wormhole, so unlink it first.
Link wormholes on a Paint a Galaxy map Paint a Galaxy
On a map for Paint a Galaxy, link two selected systems with "Link as wormhole pair". The mod opens the pair on day one. "Unlink wormhole pair" removes it again.