Red with yellow stripe is the memory wire (from the 5A BACK UP fuse):it's supposed to be hot - so that ain't it.
I would wonder about pinched or damaged wires from the rake kit. Issues with how the clutch-side switch cluster wring was handled while the bars were loose from the tree, and or some other introduction of a pinch/cut opportunity would be my first look. Also - how was the turn-signal cancelling switch addressed? The speed sensor wire there can feed back to the ALC in the radio, though it doesn't really sound like your trouble...
This all sounds more like the "tuning" switch (red with black stripe or yellow with red stripe) has been pinched to ground and the cassette is trying to change direction -- on the electronic cassette mechanism decks, the "direction change" will complete before the deck is "allowed" to shut off -- so if your deck is doing something other than ejecting with the key off... It may be trying to switch directions -- leading to my thoughts on the grounded/pinched wire (to the "tuning switch" in the clutch cluster).
I don't have a bike that has the electronic Cassette eject in the shop right now, but I kinda wonder if someone here couldn't dulplicate your issue -- Radio set to play the cassette, finger holding the clutch-cluster channel button down, then shut off the bike to see if the cassette runs a motor (all without releasing the tuning/direction switch...) ??