First, check out what's available in the way of styrene stock, both Evergreen and Plastruct carry a variety of plastic strips with various different cross sections to them. I routinely see styrene strips ready made with a 90 degree bend molded into them that runs the length of the strip. 45 degrees is a pretty commonly called for angle on things, so there may be similar strips in either Evergreen's or Plastruct's catalogs that have a 45 rather than 90 degree channel in them.
If you want to try the method you mentioned, I'd try it this way:
1. Line you parts up as you were planning to and secure them in that position.
2. Take a razor saw and make some cuts (not deeper than 1/4") along the parts junction perpendicular to the direction of the seam.
3. Take the components apart and wash the saw dust out of them so it isn't floating around inside the completed model.
4. Resecure the parts as you had them, using the cuts as a guide.
5. find some sheet styrene of a close width match to the saw cuts and paint it the interior colour or something suitably dark.
6. Cut the styrene into peices big enough that they will completely fill the cuts and leave some overhang.
7. Run a bead of medium thickness superglue along the junctions of the styrene chunks and the cuts they fill.
8. once its set, shave off the styrene overhangs and smooth it all out with the filler of your choice.
That should give you a much more secure join between parts than just shaving out a bit off the parts edges.
It's sort of like plywood, you know, strength being gained from multiple layers with their grains running in differing directions.
Hope thats helpful and that I was clear enough in my technique description.