<p>How do you estimate a <a href="http://en.wikipedia.org/wiki/Enterprise_application_integration" rel="nofollow noreferrer">EAI</a> project using Function point?</p>

Well given that FP counting is based on storage and end user interface, not sure if its even meaningful for EAI (from what little I remember).
I would say you can't, at least not in a useful way. FP counting is generally viewed as a dubious practice of varying accuracy, doing it to an integration project would just add more fuzzyness.