Complete new harness - as I re-read your thread it appears you are trying to mix the two and maybe even using the original ECM? That is certainly a challenging way to go.
My recommendation would be to advise you to use the complete new harness - & the new ECM too. You need that (& the new instruments too).
Seems like the hybrid
could work but certainly not trivial.
Things like the air idle control will be problematic I would expect.
I guess it's possible to integrate the old ECM and just use the effectively new sensor locations (in which case you would ignore the 02 of course) - you would have to develop your own tune - I guess starting with the pre-02 and modifying from there.
Incidentally there is a separate cable available for the regulator which you may find helpful - there is one laced into the harness itself but this was subject to a service advisory & replaced with an external one of higher current rating. Incidentally if you look at the pic of my bike from the right side, you can just see the regulator protruding below the side panel - on the outside of the battery box, just below the seat (seemed like a good location where it could get good air cooling)
My earlier comment on the fuel level sensor applies to the late harness & ECM of course.
Here's the radiator integration
I used a filler neck off a Honda CBR1000RR -
I just scoured E-Bay to find something suitable. I'm sure there will be other choices too.
My new engine's hoses lower hose to water pump Tee's off at the bottom & comes back up to that small connection below the main return from the head - then later still model, hose configuration has a separate small hose that connects directly into similar location as the upper of the two bottom connections on the old radiator and of course there's no TEE off the bottom hose, just one piece to the pump.
I just left the hoses of my new motor as-is (with TEE at the bottom) and plugged off the upper of those two bottom connections on the radiator; however you could equally use the later bottom hoses and connect to both. (look at the parts fiche on Bike Bandit & you'll see the difference between the hoses)
Either way is fine, especially if you already have the hoses from one or the other.
For the top connection, I was able to cut a section from one of the old original hoses that gave me the almost exact shape required with the bends.