Cheers to you my fellow Ole Codger.

My 07 Classic went through the same pains. I must have also injured something while pulling the plenum and air ducts on mine too. Can you imagine, I had to run the back of the dragon with an unpredictable throttle during RAA 2017.
Under the gas tank, there is a black plastic unit/sensor which has a tube connected to it on the bottom. This sensor (the MAP sensor) was attached to the plenum. The RamAir kit has a clamp to attach it to the fuel rail. There are vacuum tubes that come from the throttle bodies. Make sure that they are all well set. Also disconnect the electrical connection to the MAP sensor, add a little dielectric grease to it and reconnect it. I lubed all the connectors that I could get my hands on. Eventually, I replaced the TPS and MAP sensors.
Also; on the front of the throttle bodies there is a little "stepper motor" It has a rubber cover on it's bottom. Lift the rubber edge and squirt some lubricant in there. WD40 works for me. Also lube all the moving linkages on the throttle body mechanisms. Make sure that all these parts and cables are moving freely. Don't touch the factory set TPS on the front of the throttle bodies. Do all this with the tank propped up. Also, lube the connector of the Barometric Pressure sensor which is hidden on the back/right of the air box. Also lube the crank position sensor connector in the upper/back of the motor. Check your TPS and ISCV values with the motor off, as probably you have done. Run "reset the adaptations", say a prayer to the motorcycle Gods and start her up. The best pictures of all these procedures are courtesy of Warp. I think they are in the thread Connection Problem.
Steve "OlBull" is witness that these electric gremlins can be scared away by wiggling cables under the tank while the bike is running. I now carry an old Android phone, tools and cables to revive the bike if it were to fail while traveling. Like you, my opinion is that we, gremies in the art of motorcycle maintenance, injure the Rocket while removing the plenum and air ducts. I don't think it is a TUNE software problem but a poor or loose electrical connection, a bad sensor or a leaky vacuum tube somewhere. The reward of being able to fix this problem by yourself is worth it. Sort of like when Tom Hanks in the movie Castaway gets a fire going.
Good luck and have fun. The Rocket can be temperamental. If you want a zero maintenance bike go buy a new Valkyrie. It's half as kool as a Rocket but usually have less problems.