The saga continues...
I called AA and asked that the situation be straightened out and they reissued the tickets for both translant trips.
For the translant trip with miles and copay upgrade they pulled the 25k miles from my account, charged my CC the $350 copay, and sent me a receipt. After all that the AA site trip listing still shows "Mileage upgrade Requested"
The September translant trip with the SWU is from CDG, so there's the French Luxury tax for upgraded flights. AA charged my CC the $59 luxury tax, pulled the SWU from my account, and sent a receipt. The trip listing now shows "Systemwide upgrade Confirmed" so that one is good.
Today another translant trip in April where I had a SWU upgrade requested is allowing me to select seats in Biz class. That listing still shows "Systemwide upgrade Requested".
Reading other threads here it definitely appears that AA's upgrade management software is having a bad month...