Trunk open warning

Are you talking about the motortrike trunk or the original upper trunk? If the upper, I know you said you adjusted the latches but many times that is the problem. They get moved because folks think they need to be slammed closed. If they are adjusted properly, you merely have to let trunk drop closed. Try adjusting the latches one more time. Loosen the 2 screws for the latches on trunk lid and pull latch out as far as it can go. Do this for both sides. Then tighten it and try it again. Bonus will be that you should now be able to drop lid from a few inches up and it will close with out slamming

And if that fails there is a grey 14 pin connector under the seat. In it is a brown/red wire. It is unclear whether it would need to be disconnected or grounded but 1 or the other should turn the warning off.

You can also remove the panel inside the rear of the trunk that covers the opener unit. Make sure the switched are operating properly. There may be a wire loose on one of the switches is misaligned or not being triggered.
It's also possible that the wiring harness near the right trunk hinge has a broken wire.

The hoops open the switches when the lid is closed. If the hoops don’t open the switches, they are closed and grounding the circuit to make the warning come on. If you can’t get the hoops to open them, then simply unplugging the switches will kill the warning. Keep in mind, that if you unplug them, the control unit will be able to lock the trunk without the lid being closed, this may screw up the latching mechanics.