Not what you're looking for, but on a similar topic:
I wanted to use the TC* timers to create a software servo library but I couldn't find out how to use the timers so I ended up using the PWM clock to generate the output.
While testing the PWM pulse I used attachInterrupt on the same pin to measure the pulse timing, effectively creating software interrupts. It's a hack, but if you're interested the code is here: http://arduino.cc/forum/index.php/topic,130631.0.html
It doesn't use any registers, so I can't tell you about those - just add attachInterrupt()