Clunk noise on the 1/2 shift in an A999 trans.

I think TB has nailed it.
There is nothing in the geartrain that can clunk. It has to be coming from the rear end and telegraphing up the driveshaft.
Before you do anything, tighten up the rear. It may be a crosspin getting ready to launch thru the fuel tank, Or it may just be the pinions are worn out. Sometimes extra washers here and there can tighten those up for another go round. Or it may be even simpler; just bad U-joints.
Then take her for a roadtest.
The clue for me, is that it doesn't clunk when under full power, cuz this tightens everything up.

On another note, I don't think the 2-3 has anything to do with it, cuz when direct comes in, it simultaneously deactivates the band using the same circuit; so all slack is taken up in those two mechanical lines. Except perhaps on a poorly timed lift-shift, as mentioned.
The 1-2 maybe.
The whining is in the planetaries, and is somewhat normal in high-mileage units. I've had some real screamers in 904s,..................................... in winter,lol.It didn't seem to affect the longevity of the trans tho.