Woody,
What kind of KB training are you doing right now? Is it more strength or endurance focused? The FTK is a rather comprehensive program that uses the 2/1, upper/lower split, strength training approach (TRX Lower Body, TRX Upper Body, rest one day) with a six-day per week running program. I wouldn't recommend doing KB and TRX training on the same day as you will likely wear yourself out quick, but there is still room for both tools in your program. I am not a big fan of running on treadmills and running outdoors is limited here, so I've been using Keith Weber's "Extreme Kettlebell Cardio Workout" for cardiovascular and muscular endurance and the TRX for strength training. I'm a big advocate of the FTK as it is, but I think you'll find that there is enough flexibility that you can tailor it to fit your needs. I'm not sure what your specific goals are, but if you don't have any running-oriented goals, my recommendation would be to follow the FTK TRX program and use a 16kg KB cardio program in place of some of the running. If you start feeling like you are overtraining, you can always back off the KB frequency for a bit and run more to give your muscles, particularly your shoulders, a bit more rest.
"Teaching is only demonstrating that it is possible. Learning is making it possible for yourself." - Paulo Coelho