As high as possible. On my old KDX some turkey had drilled holes in the side. Which meant it was as waterproof as a a Morris Minor going over stream crossings. Obviously this doesn't worry a Motard.
I will mention that given the decent intake & the correct jetting there will be no improvement from extra holes. If extra holes make an improvement it will be as the jetting was too rich from std (often the case for safety) &/or the intake noise is noticeably increased. You can get to the point where there is no more restriction to the power from varying intake size but more will require richer jetting for no benefit in power. Henk's point about more filter area on a dirt bike is valid though.
Holes make pretty crappy intakes btw. Flat sharp edges (with no smoothing ie: drilled in an airbox side) flow badly compared to rounded intakes. However these can be over restrictive to meet noise stds. Many bikes lose power if the intake trumpets are merely just removed.
On old bikes (like TS I'd imagine) the airboxes are so small they are restrictive.
Don't you look at my accountant.
He's the only one I've got.
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