I added another tray InputSlot definition. By scouring other PPD's and the cups wiki I found that Tray3 should be MediaPosition 1 on this printer. It is different for other models, on one model it was 7, go figure.
*InputSlot Tray3/Tray 3: "> setpagedevice"
Then I change the InputSlot save
*?InputSlot: "
save
[(Tray3) (None) (Tray1) (Tray2)]
statusdict /papertray get exec
{get exec} stopped { pop pop (unknown) } if = flush
restore
"
Then to be safe, I copied any references to Tray2.
*% Tray Constraints
*% ==================================================
*% Tray 3
*% ======
*UIConstraints: *PageSize Env10 *InputSlot Tray3
...
*NonUIConstraints: *CustomPageSize True *InputSlot Tray3
*NonUIConstraints: *InputSlot Tray3 *CustomPageSize True
...
*%------------------------------------------------------------
*UIConstraints: *MediaType Labels *InputSlot Tray3
*UIConstraints: *MediaType Transparency *InputSlot Tray3
*UIConstraints: *MediaType Card_Stock *InputSlot Tray3
*UIConstraints: *MediaType Envelope *InputSlot Tray3
After that, from the windows clients I could see Tray 3 in the Device Settings tab. And once I authenticated, I could actually change it to Legal paper, yay. One caveat to watch out for, I had to edit multiple ppd's. I had to do this for the ppd in /etc/cups/ppd, the one in /etc/samba/drivers/W32X86/3 and /etc/samba/drivers/W32X86
Good luck.