Hello,
Yes, the gear box is very similar to NT1 one, but regrettably the spurs are not the same. On MTX-5, second spur is 47 48 or 49T. On the NT1, second spur is 53 54 or 55T. Ratios are completely different. Besides, with less teeth on the second spur for Mugen, each tooth of the spur is more used. Look your pinion 15T and your pinion 20T on your clutch after 2 3 liters, you will understand what I want to mean about the wear when we have less teeth.
Anyway, until Mugen solved this matter (I stay thinking its mainly a material problem), may be some guys (Seisick, TomB...) can have some tips to well align the engine (parallel to the gear box axle) and to avoid the stripping of this second gear.
Good day from Paris, guys.