The great idea about instance colors made me think of something I did with DynEQ, so I took the idea further. Let me introduce
Slave Families / Link Channels by Color!
http://b.link/mrelwood_LinkEQ_0v81
The way it works is that the Master only controls Slaves of the same color. (Black Master controls all colors though.) This way you can have 9 separate Slave families, with one Master in each of course.
You can now adjust the individual node link strengths in Single mode as well. Zeroing them out before switching to Slave mode or different Slave family makes them stay in manual control, and they won't lose their values.
Adding a node in Slave mode automatically sets the link value to zero.