I'm hoping that the King Cobra you have is the joint venture with Volvo one and not the pure OMC cone clutch one....by the boat's year it should be...
The bad spot you are referring to...this is wood rot and you need to cut out as much of the rotted wood as you can...the treat any new wood you install with CPES (thinned epoxy)...wood rot spreads because of the rot spores so you also want to treat the surronding areas...the solvents in it are REALLY strong so use a good 3 M fume respirator...gloves..goggles...
I'd probably want to remove the seats...rip out the carpet...inspect the whole deck and repair any suspect areas...then coat the deck in Durabak or similar....get rid of the carpet it does nothing but cause rot...and when reinstalling the seats put 3M 4200 on each screw to seal out moisture...
see
http://www.rotdoc.commy one bad spot turned into a deck replacement and stringer repair....now the boat is solid as a rock but man o man was it a lot of work....
Bimini tops are easy to find...I put a Taylor Made 6' long 46" high one on my '88 200...I used the slider mounts inside of the gunnels on the coaming panels so I can slide the top foward and back for more room when fishing...
The windshield....it depends on the supplier...unfortunately Taylor Made does not stock them for a long time...but Water Bonnet does...I got glass for mine when it was 17 years old...see if you can find a label or trademark on the glass that you have...I was able to e-mail FW and they told me how to find out who made it and I got in touch with Water Bonnet and bought the glass directly from them...installed it myself...