OK, so there's something to be said for quality of construction. After testing the Berlin Branch at a nominal 2% grade and not seeing any significant improvement, I took out the line altogether. I picked up a Woodland Scenics 2% Incline Set. For those that haven't seen these, it's a steady 2% grade cut out of white foam in 2' long sections.
To make the 2% grade work, I'm going to have to put a slight incline on the mainline deck as well to get over it. Right now I have about 1.5" to 2" clearance depending on exactly where I cross over the Berlin Branch. I felt this was a reasonable compromise.
The last change I made was in the geometry of the branch itself. It's now a constant 28" radius, and instead of going through an 'S' curve (with a turnout to be between the reverse curve), it has a much longer straight section with a curve at the base of the hill. I didn't want to pull up the roadbed in the yard, so it took a little bit of creativity to rework the yard throat.
Anyway, so everything's in place, and I tested it once again. The 44-tonner pulled 5 cars the whole way, but struggled at the very top (in the middle of the curve). It had no problems with 4 cars. I also tested what I've found to be my most free-rolling car, a Tangent G31 gondola, and compared it to my test cars. It rolls down the hill significantly easier and faster than the other cars. So when I get around to reaming and checking gauge on the rolling stock I think the problems will be fully solved.
Had this not worked, the next experiment was going to be a bottle of Bullfrog Snot to see how well that would work. I may still consider that in the future, with the helixes and all. We'll see.