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Fixing a bad ISB (Input Shaft Bearing) on the transmission involves tearing the transmission apart in order to get at the thing. Not super hard to do, but time consuming and does take some specific tools and some real fiddling with some bits.
An ISB will make noise with the car at idle if the clutch pedal is not pressed. If you press the pedal down, and the noise slows down (and drops in pitch) and comes to a stop, only to go right back to where it was when you let the pedal out, it's the ISB.
Your description doesn't match what my ISB sounded like in the 90 CRX I used to own. Mine was more of a rattling noise, not a squeal.
The good news is that replacing the clutch and associated parts isn't as expensive or as much work as tearing down the trans. The bad news is that it's still a lot of work, or relatively a lot of money to have the clutch replaced. If you can find a shop that will do it for less than $350, you're getting a bargain and should ask what kind of parts they use...
Window tracks weren't that bad as I recall. Not sure if the 98 Civic has the same sort of window mechanism as the 90 one did, though.
A bent dash isn't a good sign. See if you can (SAFELY!!!) crawl under the car and look for bent/torn/wrinkled metal. Also look in the engine bay and the trunk and under the carpets and such.
If the car drives nice and straight, it may not have affected where the suspension mounts to the car, which is nice.
-soD
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