Hi,
You can use the HDLink with the SDI output of your Kona 2 and this will work fine and provide you with low cost digital monitoring via an LCD display.
In regards to slot 2 being obscured by the size of the AGP graphics card, you could try another model of graphics card which does not obscure slot 2. I know some of the newer PCIe cards from both NVIDIA and ATI only take up one slot and maybe there is a newer AGP card which would fit one slot. Unforutnately I found this difficult to establish by looking at the two web sites but I suspect there is a thinner card now for AGP slots.
Regards,
Luke Maslen
Blackmagic Design