I am using Persian digits because the font lacks Latin digits as I mentioned.  If I use the \definedfont approach, I don't see the character ۴ (argument of \high) at all.  With the typescript approach, the same character is typeset but is not raised; it appears on the baseline but with smaller size.

Any ideas why this is happening?  Could it be that some parameters, for instance, \exheight are not properly set/read for this font?  Actually, I looked at the non-math fontdimens in syst-fnt.mkiv, and everything except \slantperpoint (expected) and \exheight (awkward) is non-zero.  I don't know where \exheight comes from—perhaps from the height of glyph for 'x', which the font lacks—however, \emheight is 12pt, although the font also lacks a glyph for 'm'.

I am also attaching the font in case that helps.

Thanks,

Hossein