First off I want to give all the credit to alpine fj for his write up on the subject, here is the link to the post for others having the same issues.
www.fjcruiserforums.com
I finally got the nerve to fix my leaking clips under the upper windshield frame. I had already ordered a new one and the new clips to replace the old leaky ones. I took a filleting knife and cut all the old uratheane sealer loose before removing the upper frame. It took about 20 minutes or so to cut through to where the frame would move. It came loose fairly easily but I think I broke the middle clips, so to those going to reuse theirs be careful with the two middle clips.
Everything was dirty and nasty once I removed the white upper frame, very gross. I cleaned everything up and replaced the four clips with factory parts.
The BAD
When I was removing the last clip my screwdriver pressed slightly against the windshield and crack it, terrible outcome. I will have to replace the windshield now, it had a lot small scratches and maybe overspray so it was hard to see at night. I am kinda happy about getting a new replacement because I really screwed up. So be careful when you are removing the old clips.
Since I need a new windshield now, I was not going to put on the new white upper frame because they would just break it taking it back off. I lightly tighted the screws in the clips and called it a day. It came a hard rain shower a few hours after I changed the clips and Unfortunately the of the driver side a pillar was still wet. So it’s still leaking! Cracking the windshield may have been a blessing because I would have put it all back together and still had a leak.
Now where could it be leaking from??

Leaking windshield after replacement-Solved
My windshield leaked after having it replaced. It was leaking somewhere from the upper driver's side corner. It would leak water down the inside of the plastic A-pillar trim piece down the drivers left kick-panel onto the floor. I had a devil of a time finding it. It would seem to be worse if it...
I finally got the nerve to fix my leaking clips under the upper windshield frame. I had already ordered a new one and the new clips to replace the old leaky ones. I took a filleting knife and cut all the old uratheane sealer loose before removing the upper frame. It took about 20 minutes or so to cut through to where the frame would move. It came loose fairly easily but I think I broke the middle clips, so to those going to reuse theirs be careful with the two middle clips.
Everything was dirty and nasty once I removed the white upper frame, very gross. I cleaned everything up and replaced the four clips with factory parts.
The BAD
When I was removing the last clip my screwdriver pressed slightly against the windshield and crack it, terrible outcome. I will have to replace the windshield now, it had a lot small scratches and maybe overspray so it was hard to see at night. I am kinda happy about getting a new replacement because I really screwed up. So be careful when you are removing the old clips.
Since I need a new windshield now, I was not going to put on the new white upper frame because they would just break it taking it back off. I lightly tighted the screws in the clips and called it a day. It came a hard rain shower a few hours after I changed the clips and Unfortunately the of the driver side a pillar was still wet. So it’s still leaking! Cracking the windshield may have been a blessing because I would have put it all back together and still had a leak.
Now where could it be leaking from??