Let me try to answer to all of your questions at once.
If the code has already been once uploaded from an ECU with similar typecode then you can use the harness connector to reprogram your ecu. There is a lot of interface products available on free market ranging from 20-200usd. At some point later I will make instructions avail to rewire the renesas e8 programmer to a such a device. That means literally just connecting some harness connector pins to the programmer. You can do that while the ecu is on the bike.
If your ECU has an ID number that has not yet been "opened", then a small area at the back of the ecu must be revealed for you or someone else to upload the prorgram for you. This is easy to do as dyi and also persons like RR do that as a service. To upload the ECU code you need a special hardware interface which costs again around 20Usd, but that is not (yet) publicly available as a consumer product. Anyhow building instructions are there on activeboard forum. At later stages someone should consider start building those devices.
There is both fuel and ignition cut limiters and yes you can set those individually. When exceeding the limiters usually both 2&3 injectors are cut out.
In the engine simulator for testing all the changes I am doing I use some small transformers 32Ohm to simulate the load for injectors and coils. A simple resistor does not fool the ecu to think that everything is ok. Also I learned that one coil for the injectors is not enoug, I need individual coils (which I still need to get for the injector side). The coils have both inductive load 10uH which means that it will release energy which ecu recognizes as a signal of deciding if the coil is good or not.
The 24-1/1 is the crankwheel signal. There is 24 tooth wheel where one tooth is missing, during that missing tooth the ecu receives the cam signal during every second cranksaft revolution.
Yep - its quite interesting to verify that some of the rumours presented on this board and other boards are true, where as some others are not. E.g. someone has claimed that the fuel shut off happens in cylinder 2, that is not true its both 2&3 when limiters are exceeded. Someone claimed that there is a separate ignition map for gear 5 and gear 6. That is not true (most likely) as all I have seen is that 5th&6th gear share maps where as there is a top speed limiter at around 10050 rpm. The vacuum control valve works from 0-2500rpm (gauge). When revvin the ecu on neutral gear it seems to miss the ignition at 4,6,8&10k points like Suzuki had deceided that otherwise the revs will go up too fast without load.
What is the model number on your K4 USA ecu ?
The ones I have opened and uploaded the code so far are:
32920-24FK0, 112100-1100
32920-24FG0, 112100-1070
It would be interesting to find out that how many ecus must be notched to get all the code variations out of the ecu and found out persons who are willing to start offering the notcing and code uploading service from Busa ECU:s. Whoever is interested I will help him/her to be able to start that.
Like said reprogramming is easy when code is available. Basically just purchase the E8 programmer from renesas, download the software from www.renesas.com/fdt and move the Yoshbox COS&COV wires in your harness to new places and hook the programmer to those and you are ready to go. (Obviously you loose the Yoshbox capability of your bike, but who cares with this stuff 
To do that you do not need any special skills. Quite contrary, it is as easy as any other remapping method used.
