bummer.....I hate it when it feels like you take one step forward and two steps back.
I am sure your aware of this but just incase your not....I figured i would mention. buckets seats in a bench car are not a direct bolt in. they dont line up with the same holes that a bench seat uses. there are dimples in the floor pan where the bucket seat mounting holes would be located that will need drilled out. also factory they had metal plates welded over said holes to beef up the floor pan in that area so if ever in an accident or due to years of wear and tear ...your seat tracks would not rip or beat up the metal. when I converted my duster over to bucket seats I drilled out where the dimples were located in the floor for buckets and I then welded plate steel in place and drilled the hole through it aswell. I put a plate on every hole just so i know it will never get beat up or ripped ( I documented all of this in my build thread....take a look if you need too).
as for your window leaking.......taking the glass back out would be the "right way" but you can get around all that work if you don't mind cutting a corner or two. dont just smear it in with your finger. you would probably be best getting a tube of urethane sealer from your local paint shop, load it in a caulk gun, stick the tip of the gun deep into the channel that the seal is in and try to pipe it in under the seal if you can.
yes those clips are a paint in the but. I found that even when the actual removal tool was being troublesome....I took a flat head screw driver and lightly pright up on the trim just enough to slip a 90 degree seal pick tool in under the trim and snag the clip and pull . the pressure of the screw driver and pulling with the seal pick popped the clips. I did my whole back and front windshield like this because i couldnt find my tool and my trim still looks as straight as can be.
just some hints/tips. hope you can make some use out of them.
hang in there buddy. sometimes its best to just walk away from it for a day or two and cool off.