Update: Still no luck with tuneboy. After a few hours of tinkering I got it to connect to the ECU twice. I have no idea why and was not able to replicated it again

. Even when I was able to connect I was not able to load a map (even though it was the proper Keihin map) I would get a improper map error. Frustrating. I will try to reach out to support at some point in the future. I know a lot of people have had issues and I know the TuneBoy support is iffy but I do not plan on giving up.
My new valve cover gaskets arrived and I checked the valve clearances and was pleasantly surprised to find them all within spec. There was a small amount of carbon buildup on the pistons when I looked through the plug holes, not a concerning amount but I did try SeaFoam treatment. I ran her on 50/50 gas seafoam mix and found a small amount of the carbon left but nothing to write home about. Certainly would be more effective on an engine with more carbon buildup. I did however find a startling amount of slightly oily soot built-up in the SAI reed valves and system. Perhaps even enough to stop them from closing. I cleaned those out really well put her back together and she started right up. Same old problems persisted

.
I have done quite a bit of reading on many threads and in the Service Manual and think I might be zeroing in on a potential cause. It seems that when the bike is on Idle, as well as a few other riding conditions, the ECU references the O2 sensor to try to determine a proper mixture for the engine. Now I only ever experience engine issues when at idle or while cruising at RPM's of about 4k-8k which is my reasoning behind the sensor being the issue. I even read that its common to disable it entirely through Tuneboy (if I could get it to work

). I tried this
test which I don't fully trust but it came back with my sensor being bad. Maybe worth replacing.
I start my cross country journey tomorrow with plenty of stops, I feel confident that mechanically she will make it. I just worry the toll that this poor running will have on the engone over 2000 miles. Thanks again for the support Guys.
-Will