Pankake,
the output delay adjustment cannot be used for this, I have checked that. Thanks for the suggestion anyway.
Dave,
it's all different sequences, so I do need the different channels. I have checked the Samtec interfaces and it does not seem obvious to get that up and running quickly. This should be a quick-development initial prototype, so I think I will buy one Stratix IV GX with the 8 transceivers to SMA and figure out if that can do what I want. After that I will bug you again with the synchronization :)
Thanks a lot for your help, both of you!