Jordon,
Members respond when they have the time to access the Forum and have expertise or experience in the issue posed.
Since the coach sat for a long period, a small leak can cause a lot of damage over time. You should be able to cut the longer slide seals to length. The leak along the top of the slide itself needs to be sealed. Your photo #3 doesn't show what the original seal was. My 00 Marquis had a U shaped piece that ran the entire length of the top of the slide. Yours should have the same but your photo doesn't show it. Did you remove it or ?? The 00 had rivets holding it in place. A loose or missing rivet can let in a lot of water over time. From your photo #1 is looks like there are 2 areas of water intrusion, 1 above the window and 1 between the windows. That would seem to indicate leak points other than just a bad slide seal. If the area in photo 2 that you are concerned about is the loose flap in the upper left corner, I would clean behind it as much as possible and then apply a good adhesive (contact cement or Lexel) behind the flap and clamp it in place for the required time. For sealant, suggest you use Lexel rather than silicone. It stays flexible and has a much longer life. Photos of the top of the slide may be helpful.
Steve