From memory, FSDS V3.0 used MakeMDL (FS9). With FSDS v3.5.1, you can select either. The beauty is that FSX can display models made using MakeMDL and XtoMDL (FSX).
I have found that anything I could do in FSDS 3.0 I can still do in FSDS 3.51. I just need to change the settings in the Preferences, to revert to creating the MDL with MakeMDL.

As for calibrating the 2D HUD, I thought that it was explained in the manual. I have never changed that so I don't know how it is done. I'll see if I can figure it out.

Mark