I've got that plan I was working on finished. Unfortunately, it's very complicated. It also doesn't exactly match your specs.
http://www.maj.com/gallery/SpaceCaptain/Other/cajon9x20.jpg
The bottom side can be against a wall; the top must be clear.
It is possible to get trains as long as you're talking about in this space. The over-20' tracks in San Bernardino should handle 30-car coal drags.
There's no real classification yard. San Bernardino is partly-hidden staging. (All turnouts at this end are kept in the open.) Victorville is really just a couple passing sidings; as there's a continuous grade through the town, cars cannot be left on the sidings, only whole trains.
There's no coal mine because I don't know of any in the Cajon Pass area. The industries shown are actual ones from the locations. Some prototype shots:
RailPictures.Net Photo » Burlington Northern Santa Fe GE C44-9W (Dash 9-44CW) The glass plant.
RailPictures.Net Photo » Burlington Northern Santa Fe EMD GP35 The cement plant.
RailPictures.Net Photo » Southwest Portland Cement EMD SDP35 The cement plant switcher, an SDP35.
RailPictures.Net Photo » Cargill EMD GP9 The Cargill switcher, a "torpedo tube" GP9.
18" minimum curves and #4 turnouts are used at Cargill and SWPC. Those are a little small for the SWPC engine, but an SDP35 is short for a 6-axle. it should manage.
At San Bernardino, right-hand running is normal, like in most places. However, at the scissors crossover in Devore, trains change to left-hand running. This allows them to use the gentler grade for the climb, as in reality.
The grades are severe. The short segment of 4% along the bottom is much shorter than most trains, so it won't affect them so much. The 4% grade through Sullivan's Curve is on the downhill track. However, the continuous 4% through Victorville will seriously affect trains. To reduce this grade, it would be possible to not model as far as the flyover at Frost. This would remove the need to go lower than 4" above the base elevation. However, I just felt a need to include Frost, to show the return to right-hand running, and just because it looks good.
I have marked space for transitions into and out of grades. On the right-hand side, not all grades are marked because they would make the plan incomprehensible. In fact, I hope all the stacked loops are understandable. Basically, the East End Loop is the lowest level, then the San Bernardino staging. There's a single helix lap above this. Note also that the San Bernardino loops "hump" to get over the East End loop.
Red dashed lines are retaining walls. Rock formations and rock faces are also shown. I do realize that rather more vertical scenery is necessary than on the real Cajon Pass.
Scenically, Victorville should look right in proximity to San Bernardino because it's in the place of the other yard. There are two BNSF yards in town, "A Yard" and "B Yard." There is a flyover, though in real life it's single track and used by Metrolink. Metrolink, incidentally, is not included in this plan.
The wye is part of "old Summit", isn't it? Anyway, there's another option. By replacing the #3 wye turnouts with standard #6s, you can substitute the car setout track that's a feature of the real Summit. It would have a 24" radius.
I beleive the Santa Fe San Bernardino Shops were closed many years ago, but I included them anyway because shops were a requirement.