OK, I've made a few adjustments to the Berlin branch track, and I can also raise the upper deck slightly. Clearance will be below the recommended heights for a short section, but seems to work with all of my equipment. This reduces the grade to below 3%.
But the 44-tonner can now pull 3 cars, but 2 is still better. So I tested the 44-tonner on the helix. The helix is about a 2% grade, and even then the 44-tonner can only manage 4 cars with effort. 3 is better. So it appears that with the 44-tonners with a grade I'm looking at 2-3 cars max. I'll see what I can do to add weight, but I'm also still planning on adding sound decoders so there won't be much room.
The Athearn RS-3s pulled 6 cars on the helix, 10 when double-headed. That should be OK for the freights, but I'd like to get a couple more if I can. I need to order the Reboxx Exxact Socket reamer. That will ensure all of the cars are as free-rolling as possible. I haven't checked the gauge on the cars/locomotives yet either. So I may be able to make 3 cars reliable with the 44-tonner, and 12-15 cars for the double-headed freights.
Since my primary purpose is operation, I'm seriously considering dispensing with the prototypical layout outside of the major design elements. I also need to look at whether I could alter the focus of the east side of town to the Berlin Branch. If so, I'd run the mainline down and under the Berlin Branch. Because it's behind it, it will have more room to make a more gradual grade. In addition, the 44-tonners won't need to run on that portion of the layout at all. I could conceiveably extend the Berlin Branch by curving it along the top of the helix. The problem with this approach would be that it couldn't easily tie into the helix. So I'd either have to build the Holyoke freights on the shelf, or they would come by way of Hartford.
I'm still not quite sure what impact this has on the west side of town. The 44-tonners won't have to head down the grade there at all, unless I still plan on building the Stanley Power House. I could modify that so it comes off of the siding instead of the mainline and avoid the grade there as well. So that's a possibility.
I may pick up a Woodland Scenics risers to build some test grades for the locomotives.