So the noise is only there while upshifting, 2 -> 3, 3 -> 4, etc?
I'm not sure, mostly because I can't recall what gear is on what shaft, but,
The SVT trans is a twin layshaft design. I'm wondering if the bearings on just 1 shaft are worn. That's about the only thing I can come up with. Not something I'd want to fix being you can find used trans's rather easily.
Don't "think outside the box".
There is no box.