You have to re wire your Apple if you havent yet. You need a Red LED and wire that to your apple. Then You need to wire a IR Emitter LED directly to the Clark TK22. Then when you program and take hits, the Red LED you wired to the apple will blink. Have you done this yet? While you are at it you may want to adjust the IR LED in the mantlet for Tamiya specs if you ever want to battle other tanks. I think its 6mm hole 9mm back form front edge to bulb tip.

After I read this it sounded even more confusing.
Remove the Taigen IR LED, wire in a Red LED and run that up and out the hatch next to your Battle Unit.
Get a new IR Emitter, Tamiya or Clark, I got mine with my Clark TK22s when they sent it to me, PN IR005/IR010.
Install the new IR Emitter in the mantlet and plug it into the J3 port on the Clark.

I hope this is less confusing. If you already done this then disregard.