I've never heard of using oak leaf litter, where do you get this?
The rocks are based off the description given of Varanus timorensis written by D.R. King and L.A. Smith in Varanoid Lizards of the World (Pianka and King, 2004) that "Most specimens were captured on rocky coastal areas...(Schmutz and Horn, 1986)." The rocks will also work essentially the same as Retes stacks, only with a more natural look.
The subterranean hide would essentially be another ground level hide, the idea for which I got from an article about V. acanthurus in Reptiles magazine (I can't remember which issue at the moment, I can post that if necessary), that I think can easyily be adapted to a useful hide for my V. timorensis.
The stream would essentially serve the same purpose as any other water dish, except I feel it would give a slightly more natural and interesting feature to the enclosure, though it is just an idea, and I'm not positive I'll do it anyway.
As for simply drilling holes in the plexiglass for the top, that seems like it would work fine, and it would help prevent Halai from deciding to climb on the top of the enclosure. How much would you recommend?

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