You indicate rust bubbles only, but you don't mention if there is actual hole. I suspect your leak may be where the fan blower motor pokes through your firewall, as this is the area prone to leaking.
First, pull your passenger side front carpet back far enough to where your expose the firewall. You don't even have to remove your front seat to do this. Now take a hose and spray your windshield area really well for a little bit, but do not let water hit where you suspect the leak. Then check the firewall area inside the cab, and I'll bet you'll see a trickle of water running down the firewall at the base of fan blower.
What happens over time is that the foam seal for the fan blower motor / firewall rots away, and lets water in from the engine bay.
The fix is to simply add some sealant where the fan blower pokes throught the firewall, in the engine bay. Seal the foam area really weel. You may have to move some piece of emmissions equipment, but it's only a few bolts and moves aside so you can reach this area.
Also, check to see if you have a wire loom hanging right above the blower area. That's where my water was coming in on my '98, as it was dripping from there straight into the blower hole....