Hi guys. Just an update on how I went.
I've successfully modified a couple GT46s, very happy with the result. I completely removed the factory circuit board as there was no easy way I was going to be able to use it with the transistor circuit, mainly due to a lack of space. I am also using very basic 4 function NCE D13SR decoders for all my locos, they're very well priced and I've been quite happy with their performance. I personally don't have much interest in sound, but there is no reason a sound decoder couldn't be used.
What I've done is used two outputs to provide a common ground for each end. When the headlight function is activated (NCE call it F0, I don't know what's normal) the marker lights/number board lights, which are wired directly to the common positive output, light up in the direction the loco is set. This then provides the ground for the head and ditch lights which are powered through the two transistors and can then be switched on independently with outputs 3 and 4. Because F0 is providing the ground for all the lighting at each end, the head and ditch lights will switch directions with the marker lights. As a result they cannot operate without the marker lights being on. For me, that seems ideal as under normal circumstances they would be the first to be switched on. I've provided dropping resistors (2k7) to each pair of lights as the factory board had the resistors.
I've left the red markers out as I think it looks silly to have them operational when the loco is at the head of a train. It would be easy to wire them up, and I could even use one of the original switches to be able to manually turn them on and off independently to the white markers, but for the effort I'd never use them anyway.
The ditch lights are also fixed to one output, so they cannot be programmed to flash. This didn't bother me either, although with a six function decoder it could be possible.
I've also modified a couple AN class. Far easier as the wiring positive and ground wiring to each light is separate and easily accessible, so a six function decoder is all that would be necessary, but I decided to again remove the factory board, and with a single transistor and a D13SR had directional and independent marker, head and ditch lights.
I know it seems unnecessarily complicated, but independent lighting was what I was after and I'm really happy with the outcome, and it wasn't all that difficult in the end, just a bit time consuming. It also would not be very difficult to put back to factory condition, a bit of solder and heat shrink and it should be good as new!