Yes, the lamp holders are attached to the sub-harness.
I'd try some heat-shrink wrap or tape around the rubber boot before spending that much on a new harness. Another possibility is to see if anyone who installed the Triumph tachometer kit will sell (or give) you the old sub-harness, as the tacho kit comes with a new one. Then you can clip off spare lamp holders as needed.
2005 Bonneville Blue 790cc, AI removed, Staintunes RC, no snorkel, inlet enlarged, 118/40/NBZT "Thruxton" needles/1 shim/3 turns, Ikon 7610s, Ricor Intiminators, Dunlop GT501s, D9 gauge panel, tachometer.