Overall complexity? That's a good question. It really depends on your experience, but I would give it about a 3 on the complexity scale. Having said that, I do this stuff for a living. The wiring is easy, setup and motor tuning can be somewhat trying, but not bad.
Make sure you power up the axis motors for the first time with the belts off. Do not replace the belts until you are sure you have the motors under control. Run away motors is a common thing to happen on initial setup. Then make sure the E-stop and travel limits are working correctly before replacing the belts.
The old Anilam controller on my 2 axis machine went down right in the middle of a production run and I did the complete controls upgrade, including new linear magnetic scales in 1.5 days, didn't even take the job off of the table. I was in a hurry because the customer was waiting for the parts. My machine has the same motors and drives as yours. Took about an hour to gut the control panel. Then just install the new controller breakouts and start wiring.
There is nothing wrong with the Kflop/Kanalog system, and it's a good choice for your application. I used a Galil DMC-1846 motion controller in mine because I work with those all the time, and already had the software written for both the controller and the operator interface..
I'm just getting ready to post a build thread on that upgrade.