I can help a little but my first suggestion is to contact Jay at Dauntless Motors and see if he can't send you a set of the installation instructions. Their customer service has always been first class from my experience.
I couldn't find my installation instructions so I took my tail light assembly out. Hopefully I can at least help with the 5 wire harness connections to the tail light wiring. The installation kit came with three spade lug adapters that convert a single male lug into two male lugs. Three of the wires in the harness (Yellow, Green, White) were terminated in female spade lugs. These three wires use the adapters to connect to thee of the tail light connection.
The Yellow wire goes to the Left Turn Signal spade lug (LT Blue/Red wire).
The Green wire goes to the Right Turn Signal spade lug (LT Blue/Black).
The White wire goes to any ground connection spade lug (LT Brown wire).
I connected my ground to the right side brake/tail light, one connector inboard of the right turn signal. I actually connected three wires to this light assembly. There are three spade lugs on this assembly. If you look at the assembly from the wiring side so that the right tail light is actually on your left there will be spade lugs at the 11, 1 and 5 o'clock positions. The brown LT wire will be at the 1 o'clock position.
For whatever reason the kit did not use the spade lug doubler adapters for the other two wires (Red, Brown). For these they had a short 2" jumper wire that was double staked to the female spade lug on the end of the wire. Double stake means there are two wires crimped into the same lug. The other end of the jumper wire has a male spade lug on it that the original LT wire will mate with (no sexual connotations intended).
Again looking at the back of the right brake light assembly:
The Red wire goes to the Brake Light spade lug at the 11 o'clock position (LT Gray/Yellow according to the schematics though it looks more like Gary/Green to me).
The Brown wire goes to the Tail Light spade lug at the 5 o'clock position (LT Gray/Black).
Obviously the red wire tied to all the relays should go to a fused connection to the battery. The output side of the relays look like they have the same color coding as the tail light side. The wiring from the tail lights should go to the coils of the relays. They are the trigger wires. The white wire should already be jumpered to all the ground sides of the relay coils. Putting 12V on either the Red, Green, Brown or Yellow wire and a ground on the white wire should actuate one of the relays which you should be able to hear. That is probably the most direct way to figure out which harness goes to the tail light and which one is the output to the trailer connector. Putting 12V and ground across any of the wires combinations I have mentioned should not harm anything even if it is the output side rather than the trigger side.
Once you have figured out which harness is which you can actuate each relay and check for continuity between the battery lead and the output wire of the relay which should be the same color as the wire you are applying 12V to.
My kit came with a circular six way trailer plug but you can install whatever you need. Here
is a link to a site showing the standard wiring configurations for 4, 6 and 7 way trailer connectors.
It's unfortunate that whoever removed the wiring didn't want to take the time to remove it the right way. The whole thing is designed to be removable and to be able to easily restore the stock wiring configuration. Depending on where the wire harnesses were cut you may need to splice some extra wire length onto them. That may complicate feeding the wires through the grommet back in the tail light area. The void behind the tail light assembly is sealed to some degree to control moisture around the otherwise exposed electrical connections. You may want to splice any additional wire length that is needed closer to the relays rather than out on the ends. It adds an extra splice but it may aid installation. It just something to consider if you do need to add wire length.
One note on the LT wiring: I have schematics for the 2001 model year and my bike is a 2000. I doubt the tail light wiring has had any reason to change but caveat emptor