I recently purchased a house on stilts. The floor construction from top to bottom is: 
pine boards
 plywood subfloor
 R30 fiberglass between 2x10 joists 
foil faced polyiso foam board
This construction is resulting in condensation in the joist cavity. I am trying to correct this problem with the least modification to the existing construction. I can add a poly vapor barrier between the subfloor and fiberglass batts but I still need to somehow increase the permeability of the foil faced polyiso foam board. I have been told that I can perforate the foil facing to increase permeability. Is this a viable solution ? Is there a better option that does not involve starting over ?

The fiberglass batt has a light kraft paper backing which I guess is a vapor retarder. This is facing out (cold side):

pine plank floor
plywood subfloor
fiberglass batt
fiberglass kraft paper
foil faced foam

The signs of moisture (wood discoloration) are worst around areas where there are air leaks in the subfloor. For example, where two subfloor panels butt together, there is a small gap. The discoloration is generally worst near these gaps, although, there are also some stains where there is no obvious path for air from the house to enter the joist cavity.

It is interesting that you mention the insect problem. We are battling carpenter ants in the poly iso foam elsewhere in the house (the polyiso in the rest of the house is unfaced). They seem to like the foam much better than wood. If we do put holes in the polyiso foil, I would be sure to put plywood or chipboard on both sides. In any case, they (the carpenter ants) will start going for the (structural) wood joists in the floor unless I can find a way to solve the moisture problem.

I definitely want to keep the polysio where it is on the outside of the floor joists but I am inclined to believe that I will never solve the moisture problem unless I can get some vapor permeability in this layer. From what I have read, foil facing is basically a perfect vapor barrier. Right now, my default plan is to calk any gaps in the plywood subfloor, put up clear poly (plastic sheet) vapor barrier right up against the subfloor, remove the kraft paper on the fiberglass batt, and hopefully do something to get some permeability thru the polyiso. My concern is that I do not what "something" is. Dow insulation is telling me to throw out the polyiso and buy their unfaced EPS instead.

My first question is which way is the vapor barrier on the fiberglass insulation facing?  Ideally it would be facing the heated area.  Also, the foil foam board should be facing the non-heated area.  My immediate concern with slicing the vapor barrier on the foil foam would be that you would increase the opportunity for insects to nest in the insulation.
The condensation could be occurring due to the loss  of heat from the heated area to the cold area such as electrical lines, water lines, fans, etc.????
If you could send me more information I will see if I can troubleshoot your problem further.

First and foremost your problem is being caused by the fiberglass insulation kraft-backed barrier.  It is absolutely in upside-down.  The paper barrier should be toward the heated side.  If you could remove or slit the vapor barrier continuously this would greatly diminish your problem.  Your option for a perfect vapor barrier between the insulation and your subfloor would be a 4-mil visqueen.  Regarding chalking your plywood underside you may want to consider after chalking it installing firring strips to cover all joints.  
As far as Dow's recommendation they have deeper pockets than the rest of us.  I agree with you in keeping what you have.