Hi Mike, I assume your cooler is a square type, correct? (Not the older
round jobs?)

If it is indeed a cubical unit, with 3,or 4 pads, and this is the stock
pump (a 5000 is actually not that big, I use an 11000 on mine) I think
what is happening then, is that the little holes in the V-Shaped troughs
at the top of your metal Panel frames have become plugged, and not
permitting the water to flow down the the Media Panels. This is easy to
observe too, when the cooler is first started up, you can examine the
flow, and see where there are any dry spots on the pads. Directly above
then, this is where the troughs will be plugged (Most likely with Alkali
deposits.

If I am indeed correct about this, that water is lying up there, and
thats where your water is leaking from out onto the roof, then check
these holes.

Either take a putty knife, and scrape these troughs, clearing the
deposits away from the trough (A garden hose, or a old paintbrush will
work) and if that doesn't work, then take a Cordless drill, and small
bit 5/32" and drill a 1/2 dozen more holes per panel trough to let the
water flow down better to reach the Pads. I had to do this with mine a
couple of times.
Hope this helps, Mark