Here are some links:
http://www.alteraforum.com/forum/showthread.php?t=28472 (
http://www.alteraforum.com/forum/showthread.php?t=28472)
This one:
http://www.alteraforum.com/forum/showthread.php?t=24720 (
http://www.alteraforum.com/forum/showthread.php?t=24720) hints on using the serdes.
Another idea discussed on this forum was to use a GX-receiver in basic mode as a sort of 'logic analyser'. That would go up to 3.25 GHz.
How do you form your input pulse? How large are these transition times?
I assume you have a comparator or something to detect the transition-time.
You may also want to take a look at time to digital convertors (
http://en.wikipedia.org/wiki/time-to-digital_converter)