Hi Tom,
[quote user="Tom"]but do not know how to implement the math[/quote]
This is the core of any 2D/3D vector programming, not specific to MicroStation. So if your aim is to be able to write VBA macro, you have to learn it. If not, ask (and probably pay) somebody else to write the macro for you. Nearly any analysis and probably all element creation require to enter rotation (sometimes tranformation) matrix.
It's not so difficult to use the matrix (correction ... it's very easy!), because you can use it as a black box and to learn what is inside later (nothing else than sin and cos you have used already). Because matrices are the core of many disciplines, there are plenty of tutorials available on Internet. But I guess for your purposes it would be enough to check information in MicroStation VBA help like a description of Matrix3d type or "Rotating Elements" example.
[quote user="Tom"]Did you have any thought on the other issues?[/quote]
Frankly, I don't care about other errors, because I don't think they are important. My experience is it's better to correct one problem at a time (especially if it's so important/critical as the discussed using of rotation matrix) and to focus to a next one later. Quite often the first bug repair changes the code in such way it changes also other problems ... and sometimes they are solved as a side effect.
With regards,
Jan