Sounds to me it could be the third gear synchro if it's crunching nearly every time you put it into third gear.
I'm no expert but this happened to a friends celica box, everytime he shifted into third at anything above 3000 rpm, it would crunch. Pulled it apart ... bung third gear synchro.
If it is, its not cheap to fix, it requires dropping the box, taking it apart, and getting a replacement synchro (might as well do the rest if it comes to this as well). This SHOULD be done either at Toyota or by a gearbox specialist.
As for you oil ... it has ATF in there you say ? That is bad bad juju. ATF should certainly not be used in a manual box since its weight is vastly different to gearbox oil designed for use in a manual.
I use Redline MT90 (75w90) in my supra box (R154) and I would recommend it to anyone with a high performance box (except the getrag 6 speed ). You might want to try Redline Lightweight Shockproof oil and see how you go, it might or might not fix the problem. Chances are it won't but you never know! Downside to the oil is that its about $120 from Coventry's.