old tar/gravel, 3" foam & tar/gravel on top of all that?!?!?

Is this normal????

We have a leak in our daughter's bedroom following the beam (can't see the point of entry) Our roof has old tar/gravel, 2-3 inches of foam over that (put on approx 6-7 years ago according to a neighbor) and tar and gravel on top of that!

I've read the various forums here and haven't found anything about tar/gravel over foam. We have big ponding areas (one right above the leak in our daughter's bedroom) and rippling near the slight peak of our Atrium model Eichler. I'm stressed as our daughter has allergies and my husband allergies/asthma & I'm very worried about potential mold issues. A contractor said we could drill bore holes (!?!?!?!) in the ceiling to help it dry out, seal over the leaky areas and maybe get more life out of the roof or re-roof in the summer. We're not very excited by that plan. So - we're going to get roofing estimates. (We have no record & no ideas who did the foam roof with tar/gravel on top, so if there is any warranty we can't use it.)

We're trying to figure out what to do - it seems to us we'll need to re-do the whole roof in some method (When we bought the house in May the home inspector thought the roof might have 3-5 years left, so we thought we wouldn't need to worry about the roof till later on). And based on what we've read we're leaning towards foam with a waterproof membrane on top.

Our HOA says there are many duro-last roofs here that have stood up well. However, my impression is that the foam boards used with duro-last absorb water if they get wet & so you pretty much only have the membrane as your waterproofing. Also from what I've read "Acts of God" including storms, etc. are not covered by the warranty (so what's the point, right?). However, we've had others tell us to avoid the spray-on foam (not really giving any reasons we can recall) so we're really confused.

We're also concerned as we figure that we'll likely need the old roof scraped off, so that any potentially wet areas can be fixed to assure there is no mold or other problems. From what we've read here that adds considerably to the cost and also makes a big mess inside the house as well (Arrgh!)

We'd appreciate any advice, commentary,thoughts, suggestions etc. as this is our first flat roof home. We're "newbies" to all this and really want to be sure we take the right route.

What we want to be sure of is:

No mold
Exceptional water-proofing (we get strong winds and heavy rain coming off the Ocean in Lucas Valley)
Good insulation (we don't want our bills to go up & at present we have that 2-3" of foam between the tar layers.)
Good warranty with a company likely to still be in business if we need to use it.

Advice dearly appreciated!

We're in San Rafael, CA

Thanks!