I think most of your concerns are simply the change in working style. The rangefinder on the R3A is about like having a split image focusing screen optimized for a 50mm f:1.4 lens on an SLR. It may just be more sensitive than you are used to. One thing to check out is the vertical alignment of the rangefinder, which can cause the two images not to snap like they should. Find a strong, contrasty horizontal line (power lines work well) and see if they are properly aligned or if they're offset vertically. A good hard drop in shipping can cause vertical alignment to go out. Also make sure you don't need dioptric correction to see clearly. The R3A can take a common Nikon SLR diopter finder lens, but I forget the model. I find that the focusing on my R3A is slightly snappier when I have both eyes open (works if you're right-eyed, for lefties, the body is in the way).
Rangefinderforum.com has a discussion of adjusting vertical alignment on the R3A if you search for it, and either photos or a link to photos of how to do it. You do have some leeway on focus with smaller f-stops. See cameraquest.com for some information on what apertures are the limits for the R3A rangefinder at common focal lengths.
As for brightness of the finder lines, I shoot constellation photos with the C-V brightline finders, and the only light is from the stars on a moonless night. I can see the finder lines clearly (and MANY more stars than any SLR I've seen) under these circumstances. If you have enough light to focus, you should be able to see framelines.
If you get into a really dark spot, I'd take this idea:
http://www.leicagoodies.com/shine.html and run with it. Mine would be a red LED, point back at the finder frame window, and be dimmable.
You're probably doing fine on focusing.
Hope this helps,
Lee