I know I'm a little late to this issue but I feel the need to weigh in:

I've gone through this intersection every weekday at least once for almost 10 years now and have seen more accidents here than anyplace else in the city.

We've got lights warning South Bound Frontage Road drivers of the impending stop light, and those work great.

The first time I drove west on Mountain from under the bridge I almost did not see the traffic lights at all. I think it's a combination of the traffic lights proximity to the bridge and the lighting that distracts drivers headed west. The lights are just not in a place one expects them to be, and if there is no traffic around you, like there often is at this intersection, there's no other cars that give you cues that there's a light there. I may be over-analyzing it but that's my reasoning for almost killing myself that day. (See attached photo for something similar to what I was looking at, imagine the sun setting west and it could even be worse).

However... most of the accidents I've seen seem to have been caused by somebody running the red light on eastbound Mountain. Obviously there is a high school nearby, could that be a lot of the problem?

Perhaps a combination of flashing lights under the bridge and increasing the yellow time for eastbound Mountain. And an public awareness campaign at Albuquerque High? Perhaps a sign reminding them of the amount of accidents that happen at this intersection.