Hmmm, autotune needs O2 sensors and the Autotune module. Do you have both of those installed? Otherwise that would explain why trim values would be greyed out. I can attest to the online maps being too rich for these bikes.
If the pulsing is the engine surging, do the ground fix. This is a must on this bike for it to run "right":
Don't try to short-cut this process, make sure the connections pointed out are paint free, clean and tight. Put some dielectric grease (pooky or maybe poookie) on the connections to keep moisture and oxidation at bay. Galvanic corrosion is a reality and it does affect these bikes, so servicing these connections can be a yearly thing if you are in a humid area.
If the problem persists, disconnect the PCV from the system and take it for a spin. If the problem persists, at least you know what the problem is not. Make sure the PCV is not using the "vampire" connector to get power, This is a common failure point for these installations. Make sure the PCV has a good solid connection to power. I soldered mine in place. Never had an issue.
Really the best way to get a solid map with these units is to put it on a dyno and have it tuned. Autotune (if installed) will fine tune a close tune, but it takes a long time for autotune to get it right from a bad tune. There are too many scenarios where the ECU runs open loop to be able to Autotune properly from a tune that is too far off.
If it's not the engine surging, but is drivetrain, then as Spike indicates, start looking at wheel bearings. The drive shaft on these are not too difficult to get out so if your wheel bearing check out okay, that might be the next thing if your bearings check out okay. You should probably pull the rear wheel to check those bearings anyway, so it's not a huge effort to get the final off and the drive shaft out to check the spines and u-joints. Make sure that on re-assembly, all splines get some moly paste (available at the Honda stealership). One tube will go a long way. Many will tell you that a good synthetic grease will work for this, but it is not as good as the moly paste the service manual calls for.
You can download a service manual for your bike from here;
I actually printed this out and put it in a binder on the shelf in the garage. I find a printed manual preferable to a PDF when in the middle of a project.
Best of luck, and welcome to the board. You will find the people here very helpful and incredibly knowledgeable regarding these bikes. Never be afraid to ask if you need help, we have all had those "DUH!" moments.