True that this bike has CAN bus but as a general rule, and as applied to the things that the original poster mentioned adding to the bike, it would not make any difference. In other words, while the bike does have the technology on board and it is used in some places (CAN bus), unless you accidentally cut (read: hack) into that system it would not make any difference in adding farkles. This is very much UNLIKE something like a BMW which uses CAN bus to control turn signals and several other 'normally just 12 volt electrical systems' on their bikes; Kawasaki only uses CAN bus between the main ECU, the KiPass ECU and the instrument panel (and even then only for the gauges and I believe one indicator light). There is no aspect of Kawasaki's use of CAN bus that anyone would ever need or even want to tap into to the best of my knowledge. So in the end, the electrics of a C-14 really can be treated just like any other <non- CAN bus> technology bike such as an ST1300.
To the original poster, I don't even know what to make of what you have posted. The symptom set is not like anything else I have ever heard of. It almost sounds like you may have multiple problems with each one causing specific symptoms that don't correlate to the other problem(s).
I especially cannot understand the need to turn the bike on twice to clear and FI error display screen. Also the blown fuses would indicate that at some time there was at least one short somewhere on the bike and that may have led to some of your current problems (whatever caused the fuse to pop did some other damage and just replacing the fuse did not fix that damage).
This really does sound like a complicated problem to diagnose and while I would gladly help you out of I could, I do not even know where to suggest you start looking for this problem(s). The only thing I would say will sound pretty silly but I would take a meter and start probing around 'just looking' but I do not think anyone could even begin to build a diagnostic plan for whatever you might find along the way. Sorry but I think this one will have to be dealt with 'in the flesh' rather than across the 'Net. I am not saying this because I am trying to shoo you away, just that I don't think you will find any really useful suggestions for such an unusual and logic defying situation.
Best of luck with it though and if you have any specific questions I am sure we will try to help you out as best we can.
Brian
The key word here is 'old 07 Honda ST1300'. This isn't your grandma's electrical system on the C14. It uses CanBus technology and while very modern it can dislike electrical additions such as farkles. You have to be careful where you splice in and the connections have to be super good otherwise the gremlins can get in.
I agree with the dealer on this one (very rare for me to say that as you did the farkelizations and the bike wouldn't start after that). It's unfortunate for sure, though.
My only advice that I can give is to remove all the accessories and see if the starting problem goes away. We've seen bad grounds cause all kinds of mischief. You have to be careful where you ground this baby. Get a meter and make darn sure you have a good connection back to the negative terminal of the battery. The rear end of the bike has been notorious for poor grounds (using aftermarket farkles).