I made a custom fixture to do the pistons while they are in the motor, in the car...I also made the custom cutters, however ISKY does sell a cutter that uses your head.
Alright, you can use your old heads and an old valve to do the notching. Just cut teeth into the valve with an air cut off wheel. Bring the piston to be notched to TDC, put the modified valve ion the head, bolt it on, and chuck up the valve stem in a drill. As far as knowing how far to go, just keep checking. You should have some idea how far you need to go before you begin. Then just keep setting up your valvetrain and checking till you get there. Once you have the first cylinder done, you can make a mark on the valve stem and simply go to that depth on the others. You should remove the valve seals first, as they can be at different heights. The reason I asked if you have new heads, is you are gonna need new valve seats for sure.
How's that?
I think your asking since the large valevs fit with a TW can you do it with a stocker? Well you can not put a 2.02 valve in a stock head, plus the larger valve will kill the flow of that small head.
The TFS fits since the valve location is Twisted, which moves it away from the centerline and actually allows for a slightly larger cam to be used.