Just keep your EK9 box, put the 4.928 Final Drive in and switch to some Carbon-Moly Synchros
The fact that you are contemplating using the 4.928 Final Drive leads me to believe that you are after acceleration and not top speed. A higher top speed is the only advantage the ITR '98 Spec box has over the EK9 box (same as ITR '96 Spec) + 4.928 FD.
or get a 98 spec gear box replace 4th gear with that or 96 spec dc2 or ek9 and then u have great 1 - 4 gears and a nice 5th for motorway use... i have that done in my 00 teg