Just got off the phone with Yamaha Customer Relations at (800) 962-7926, press "1" for Star Specialist...I talked to a Specialist and reported the issues noted both here and on other Forums regarding the Orange and Green/Red ignition coil primary wires being crossed on some bikes...and noted the poor starting and running below 40 mph.
Before he'd answer I was asked for the second time in a week for my VIN and mileage (he fills in the form when we call)...the person I spoke with looked at the online Yamaha known issue database, and noted Yamaha has nothing regarding the coil issue formally on file.
He suggested owners that have experienced running problems, that may or may not be related to the crossed coil wires, contact their Dealer and have them duplicate and identify the problem...the Dealer is then to contact their respective Service Rep and file some sort of notification so that Yamaha can be made aware of the issue.
So, if I were so troubled I'd at least call my Dealer, explain the problem, and let them report it to Yamaha...otherwise there will never be a Service Bulletin or whatever they call it at Yamaha generated...calling Yamaha Customer Relations as I did may not generate a Service Bulletin, if I understood correctly what the phone guy said, it takes a Dealer to initiate the Bulletin process.
I asked if Yamaha used differential cylinder ignition timing for each plug for a given cylinder (as a potential source of poor running with crossed coil wires), and was told to contact my Dealer for that information, as they will then call their Tech Rep for clarification...and that's why I believe they now omit that type of info from the Service Manual we all read, maybe just to force us to work through their system for any technical information.
On another note, I asked him if installing Yamaha's optional Speedstar pipe (like I had on my Stratoliner) without an additional fuel controller (PCIII, etc.) would harm the engine, and would the stock ECU fuel the engine properly without damage (I already had an answer from Yamaha in 2006)...his response was

that the Speedstar pipes were designed for full throttle racing, may not work in street applications, and therefore weren't recommended unless my Dealer said so :rant-rave:.
Gary in Fairbanks, and I'll let it all go for now with a big laugh.
Edit: Called my excellent local Dealer and their Service Specialist, explained the above stuff, and he told me the same thing as above...we talk to different folks than do the Dealers, and if there's a problem, it's best to have the Dealer file a complaint as it gets fixed sooner within their system than if we do the contact with Yamaha.