Lots of 'Gotchas' !
Both are the same size, bore and stroke. Rover called the 3.9 the 4.0 but it was the same.
The 3.9 GEMS engine is almost identical mechanically to the THOR, BUT has a different camshaft gear and flywheel pickup location. We have found out that our Disco 4.0 THOR has a GEMS camshaft gear, so we have to strip the front end and change the gear.
If you lay two short motors side by side, one a GEMS and one a THOR, the only difference you will see is the flywheel pickup location, and you'd need a ruler to see the difference. The ring of drilled holes in the back of the flywheel is on a different PCD to the THOR engine.
The camshaft gears are visually different, the GEMS engine has four slots, three short and one long, all curved rectangular shape. The THOR camshaft gear has irregular shaped holes in addition to the regular slots. Pictures below, THOR gearwheel picture courtesy of Barri in the USA..
The Injection system is obviously different.
Peter