I'm not familiar with the fan issues other than I've read that being 20+ years old they can be dead from age/wear now. so testing them individually or checking the wiring would be an easy starting point.   water leaks can be tricky to track down, a tip i was told decades ago was to puff flour around suspect places and it will be washed off if there is a leak. 
don't rule out water doing the capillary action of running down a wire, bonnet cable, etc if the grommet is cracked or just running down the firewall into the brake pedal hole etc (shouldn't but things like that are possible)
also the door seals can be surprising for a leak source, as with windscreen seals. 
the flour test is probably worth doing if you have a suspect spot for leaks.
the air vent is pretty tall, there'd need to be a lot of water in the plenum if it was to overflow that, and if it's been repaired in the plenum they should have seam sealed it otherwise. 
check the plenum isn't full of water due to blocked drains first, that's an easy test also  

@deankxf or @SPArKy_Dave might be able to help with this. I recall one fan came on with A/C and the other was temp sender.??  

Sadly I just hosed the car down & it still leaks, wounder if the water found it's way through top of the vent.  Another simple fix you may be able to help with my Twin AU fans only one was working, perhaps just relay or wiring you think 🤔 

from my understanding the difference between the 94ab and the 94dt (ef xr6 head) was the valve size, pretty sure they had the same port size, but I could be wrong.   I'd assume that fitting the larger 94dt sized valves to the 94ab head would bring it up to the xr6 heads flow rate.   Does any one know what the exact specs of the EA Falcon's cam is?

@Thom any thoughts on VCT heads, AU tickford heads and the XG head above?
  is the head even a restriction with a stock ish cam?

I don't have any proof other than being told that the AU heads flow better than the earlier heads

Is the AU tickford head any good flow wise.   I checked out my XG motor, it has a 94AB head which seems to be one of the better non tickford e series heads.

From what I am aware, the only difference between the XR6 head and the VCT head is the VCT.   As far as the BArra ECU, pretty sure you would be better off with individual coils.

Apologies for raising an old thread, but it's not covered here.   Is the AU XR6 VCT topend worth playing with as far as the head goes?    Would the VCT itself work with the EA cam, I'd assume if it did, the VCT when it kicks in would make the profile a bit more aggressive again compared to using the cam in non VCT cars.   Sorry for the dumb questions there seems to be limited info on hotting up an NA VCT engine outside of locking the cam and using the non VCT cams.

Is the XR6 VCT topend worth playing with as far as the head goes? or should I be looking for a different head like the EF XR6?   I have the correct EEC to suit the VCT with a 5 speed.   I was thinking of running a Barra ECU for extra tunability would it be worth going to an FG coil pack arrangement?   I have what I assume is the stock XG engine as well with everything needed to run that so swapping parts is doable for sure.