Lots of possibilities.
- I've never used a SunRace cassette but I know they're typically cheap. Maybe that shifting ramp is poorly designed?
- Chainline should be measured, not eyeballed. But poor chainline shouldn't affect the middle cogs. One of the ends will be worse.
- The rear derailer hanger should definitely be checked with the tool, not eyeballed.
- The RoadLink should be fine but in my experience it can make shifting less precise if the upper pulley is too far away from the cogs. Have you checked the b-tension?
- The long run of the RD cable on a tandem is going to exaggerate any other issues, especially if the bike is setup for full length housing. Replace cable/housing if you haven't recently and make sure all the ends are cut cleanly, housing is routed correctly, etc.

It's possible that two or more of these issues combine enough to cause the problem.