I've been mashing out these same sort of issues on a similar project. I have yet to figure out why the file comes in a few feet off, but we just leave the baseline in the drawing as a point of reference so they can move into place. I think it has to do with the drawing origin and/or limits. Not sure.
On the points can you export all your points to a point file which they could then import? Are they using plain Microstation or a civil product like powercivil, geopak, inroads, etc.? Are you just saving as to R2004 format or are you exporting to AutoCAD back to R2004 format?
Check out this thread over at theswamp to see what we've been discussing. There are some links to useful information there.