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.
Do it correct, or do it twice.