sh!te given the weather we are havin it looks like there is going to be a few fast track PHD leak engineers LOL, i have the same tissue and have got it resolved, after much searching on forum i completed the usual suspects.
New scuttle tray ( mine was cracked)
Unblocked sunroof drain holes
Used Mastic sealant to seal upper blower cover to bulkhead
Front door membranes and unblocked drian holes on doors
Replaced accelerator cable
Replaced Clutch cable
Replaced both door gutter strips
This was done over a period of time and after my recent respray i still noticed water ingress on both sides especially the drivers side coming from surrounding area of clutch cable.
As i had replaced both roof strips during the respray i needed to match the doors to seal with new strips, ( i had carpet out and cleaned and was not fitting until i got to the bottom of leaks) any way this required brute force with windows down and slight pulling on upper door so that the frame was a snug fit to the gutter, to test i got me son to sit outside with a hose until no water ingress was visible.
Time consumming it was but after a tweak here and there both strips/doors became water tight, i then noticed a steady pool gathering on drivers front well, upon inspection of drivers door seal i noticed that in lower lip mid section were seal conjoins the lip was rotten and not making a complete seal, after a bit of fabrication from a scrap bit of tin and some pop rivets it was easily retified so that a water tight seal was made.
Again i tested thorougly with a garden hose a high pressure and was pleased with the outcome of 100% water tightness.
Interior refitted etc etc and car driven for a few days until the next monsoon, this time i had parked my car with the Nearside wheels on the kerb and car at an angle, it rained that night & much to my dismay it also leaked.

I sourced the leak to above the pedal box but was lost as to were it was coming in, i got totally F***ed off at this stage and ripped out scuttle tray, wiper assembley, ECU and all cables, i then got transparent kitched sealant and a paint brush and covered every visible grommet on the bulkhead, i also used sealant when putting the cables back in, everything was reassembled and selant left to cure for 24 hours.
Again i got my poor son to blast the front screen and surrounding scuttle tray with a hose for nearly 1 hour
and happily have 0 leaks, nil nought nothing.
I know this is long winded but only 1 members experience of water ingress