I've got the sunbeams to work, but not as placed effects. Beam FX need a source and a target. As a placed effect the beam was using the same location for both, resulting in a zero-length beam.
This means that you only really need separate SEFs for the different sizes. The direction, angle and length of the beams are determined by how far apart you set the source and target objects (usually ipoints). I created a quick HB script for the source ipoint, that applies EffectBeam() to a target ipoint for 6.1 seconds every round. And voila - crepuscular beams made to order!
I've already got a light beam system for interior cave entrances that spawns and deletes lights with different colours, ranges and intensities depending on what time of day it is, as well as spawning one of the cave beam effects during the day. However now I can create dynamic crepuscular beams that change length and angle depending on the time of day, by destroying the target ipoint and recreating it in a slightly different position. The HB script can also determine what times of day the beam appears at all, thus turning it off during the night.
Now I just have to come up with an algorithm that determines the position of the target ipoint based on the hour value. A semi-circle would be more accurate, but I suspect moving the target back and forth in a straight line would be just as effective (and much easier to script). If I really strive for detail, I can set variables on the source ipoints that tell you what side of a building they are on, so west-facing windows only spawn beams in the afternoon and east-facing windows only spawn them in the morning.
Assuming that most modules will be based in the northern hemisphere of Abeir-Toril, south-facing windows could have beams all day long, with the target ipoint moving west to east during the entire day.