Thanks for your quick answer Dave!
Regarding Stratix IV GX dev kit, problem is that the reference manual quotes 12 channels with 8.5 Gbps + 6 with 3.5 Gpbs (I don't know why). That is in page 2-5. I would like all of them to have the same performance. I am also not sure about the PCI: can I just use that physical interface but custom configure the transceivers?
The DE4 is a little bit of the same: it quotes only 12 transceivers available.
http://www.terasic.com.tw/cgi-bin/page/archive.pl?language=english&categoryno=138&no=501&partno=2 So I still don't know what to do. Am I reading any of this availability in a wrong way?