Chances are your car has a 4.3:1 diff whereas the 6 speed gearbox came with a 3.909:1. As your speedo drive is taken from the gearbox and is therefore unaware of this, it's working on the assumption the diff will be reducing the rotational speed of the rear wheels rather less than is now actually the case, thereby giving you a high reading.
Easiest solution maybe to get some custom dials made up, graduated to suit, or source a 3.909 diff.
Edit: Further searching suggests the 6 speed gearbox was also fitted in combination with a 3.636 final drive. This would make the situation even more noticeable - which model did your 6 speed originate from?
Check your new dials against the originals too, UK and JDM dials are graduated slightly differently as well (on the MK1 at least).