Hello Richard.
I used a warm white bright LED with a 470 ohm resistor in series. It is very bright and illuminates the whole of the headlight. Don’t like it actually. Assuming you can actually remove the headlight from the front of the loco I would do so after drilling access holes through from the underneath. Then dismantle it and paint the inside with a couple of coats of black. Drill the LED hole from the inside, shorten the LED legs and solder the connection wires to the back of the LED, paint the rear part of the led black and glue in place with a silicone adhesive.
I have never been able to get the Thomas headlights out. Percy and James were easy to remove.
If you cannot get the headlight off you will have to drill out the silver “lens” from the front. That means (very carefully) removing the flange from the rear of the LED so you can get it in. I would do this after adding wiring to the LED so you know which is the Anode and which is the Cathode.
I was in a rush to get these last loks converted so did not take pics. I will doing an Emily soon and will show a step by step pic series.
Sorry, I have no idea how to light the eyes.