There definitely are ways to flash your ECU at home, specifically woolich racing http://www.woolichracing.com/products/kawasaki/kawasaki-ecu-flashing.aspx sells kits to allow you to flash your ECU.
In my opinion, the 3 biggest caveats to doing this yourself are:
1. Getting a proper map for your bike, in your location for your riding habits.
2. The learning curve associated to do the flash and make/tune the maps (although this can be a lot of fun if you like learning about this stuff!).
3. The cost associated to buying the kit is more than sending your ECU to someone to flash it for you.
If you'll be flashing multiple bikes or are the kind of person who likes to continue to fine tune your maps and will be using the flashing hardware more than a couple of times the kit could be the way to go. Otherwise I personally would just find someone who has a good reputation and send the ECU to them to flash as its easier and cheaper.
Alternatively, Power Commander has "piggy back" ECUs and oxygen sensors that in my opinion are pretty easy to use and are comparable to the cost of having someone flash the ECU for you (although adding things like the autotune and LCD screen drives the cost up a LOT more).
PS: this is probably better posted to one of the other topics as this topic is intended for people posting how to do something, eg if you had a step by step guide on how to flash your ECU at home that would be perfect here, but good luck with your tuning!