Tool/software:
Just to confirm my idea.
I need two leds, one to show 10/100 link/activity-blink, and another to show 1000 link/activity-blink.
Such configuration is not directly available, but could be achieved by combining three leds to two:
(Strappings omitted for clarity)

Requires following configuration for led pins and polarities:
LED_0 = 0101: 1000BT link established - Active high
LED_1 = 1000: 10/100BT link established - Active high
LED_2 = 1011: Link established, blink for transmit or receive activity - Active low
Could this work?