I can't think of any instrumental thrash bands, I don't think there are any to be honest. Some instrumental bands worth checking out though are Sleep terror, Behold...the arctopus, Dysrhythmia and the aforementioned Windham hell.
Chris Poland's (ex-Megadeth) first solo album contains some thrash elements but it's mostly fusion stuff if I remember correctly. It is instrumental though. And I guess it sounds nothing like Slayer. I personally didn't really care for it all but some people seem to like it.
Sepultura's Inquisition Symphony is an 8 min thrash instrumental...probably similar to what you're looking for...alot of thrash bands played instrumentals but none that i know of are totally instrumentals