i think your pf call of the raise is a bit loose with this hand in this position, but i doubt that it's that big of a mathematical mistake if you can play well post-flop. i think there's actually a better case for folding simply due to the fact that your relative position to the pf raiser sucks, too.
this is a very bitter-sweet flop. you've got top set, but there's a low draw out and a flush draw that's not your and you have no blockers against. this means (as monk suggested), you're probably going to be a 55/45 dog if all the money gets in the middle. as such, peeling one off and re-evaluating on the turn is often not a bad play.
that being said, since your relative position to the raiser and others in the hand is poor (and precisely why a pf fold might be called for), i think you either need to raise or fold on the flop -- calling the flop is the worst. the goal of the raise is to isolate against what is at worst a 55/45 hand. there's enough dead money in the pot so that it's only a very small mathematical error to take this offer as a dog. if you add in the fact that you might be dominating some hands and/or have fold equity to take the pot down now, i really like raising on the flop the best. calling strikes me as the worst option here because you might be pricing in some draws (or at least letting them make smaller mistakes).
i should add that the gutshot adds only a little bit to villains equity even if he has some kind of counterfeit protection:
http://twodimes.net/h/?z=1862620
pokenum -o8 9s 9d as qd - ah 2h 8s kd -- 9h 3h 4c
Omaha Hi/Low 8-or-better: 820 enumerated boards containing 4c 9h 3h
cards scoop HIwin HIlos HItie LOwin LOlos LOtie EV
As 9s Qd 9d 174 535 285 0 0 0 0 0.432
8s Kd Ah 2h 285 285 535 0 610 0 0 0.568
if villain has A25x and the flush draw, you're in much worse shape, but that's a bit of the MutBS:
http://twodimes.net/h/?z=1862629
pokenum -o8 9s 9d as qd - ah 2h 5s kd -- 9h 3h 4c
Omaha Hi/Low 8-or-better: 820 enumerated boards containing 4c 9h 3h
cards scoop HIwin HIlos HItie LOwin LOlos LOtie EV
As 9s Qd 9d 174 407 413 0 0 0 0 0.354
5s Kd Ah 2h 413 413 407 0 610 0 0 0.646
anyway, once the (seemingly) safe card hits on the turn, you really want to get it all in:
http://twodimes.net/h/?z=1862622
pokenum -o8 9s 9d as qd - ah 2h 8s kd -- 9h 3h 4c js
Omaha Hi/Low 8-or-better: 40 enumerated boards containing Js 4c 9h 3h
cards scoop HIwin HIlos HItie LOwin LOlos LOtie EV
As 9s Qd 9d 17 30 10 0 0 0 0 0.588
8s Kd Ah 2h 10 10 30 0 20 0 0 0.412
it sucks if some jacker has JJxx (that's happened to me before), but i can't imagine that that kind of hand is likely to stay in after the flop unless he holds specifically A2JJ.
anyway, i think that a flop raise is really the best play. there's a small chance that you're a pretty big dog, but there's also a small chance that you are dominating another set (although probably with a low draw).
i'll be interested to see the other hands and to see what their equities were on each street.