You can run this in one go from EigenCommander. It will add lit tonics to all instruments in Alpha Factory Setup 1. This script was written and tested against 2.0.50 of EigenD. The MIDI connections will not work prior to EigenD 2.0.50, since in earlier versions there were no light connections on the rig interfaces; you needed to add these first.
clarinet rig output light to keygroup 1 clarinet output light input connect
cello rig output light to keygroup 1 cello output light input connect
synth rig output light to keygroup 1 synth output light input connect
sampler rig 1 output light to keygroup 1 sampler output 1 light input connect
sampler rig 2 output light to keygroup 1 sampler output 2 light input connect
sampler rig 3 output light to keygroup 1 sampler output 3 light input connect
sampler rig 4 output light to keygroup 1 sampler output 4 light input connect
audio unit rig 1 output light to keygroup 1 audio unit output 1 light input connect
audio unit rig 2 output light to keygroup 1 audio unit output 2 light input connect
audio unit rig 3 output light to keygroup 1 audio unit output 3 light input connect
audio unit rig 4 output light to keygroup 1 audio unit output 4 light input connect
midi rig 1 output light to keygroup 1 midi output 1 light input connect
midi rig 2 output light to keygroup 1 midi output 2 light input connect