When you mean stripped wires, do you mean they were stripped "clean" (Someone has previously messed with them), or do you mean that the wire plastic casing has melted (electrical short)? When you say the "tupe" isn't in the right hole, do you mean the wire harness connection piece is not plugged in?
Either way this is what your outcome looks like:
Situation 1
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-You had a short in your electrical. SYMPTOMS - Wire casings are melted and some wires may be blackened, the motor wouldn't make noise like its working.
Situation 2
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-The Wire harness may have been disconnected somehow. SYMPTOMS - Your switch would make nothing happen, no noise, no nothing. That could mean that the connector is not on the switch or on the motor.
The way you described that it makes noise as if the motor is working makes it sound like a motor or regulator problem. This wire situation is odd, if you could take some good pictures of them and upload them it would be a lot easier to diagnose the problem.
As far as cost is concerned here are some numbers to think about:
IF YOU INSTALL
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-Motor - About $60 - $80, do not buy at the dealer, go to Autozone or NAPA.
-Regulator - Depends on your cars year,
1990 - 1993 LINK TO AUCTION,
1994 - 1997 LINK TO AUCTION. All are Buy It Now eBay auctions.
-Wiring - Bad News here, you have to cut and put in your own wire, OR PAY A DEALER for the door harness. If you know what you're doing go ahead and do it yourself, but if you don't, just buy the harness as it's dangerous to mess with electrics when you don't know how.
IF YOU HAVE IT DONE
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NOTE - These are based on prices where I live, Grand Rapids, MI, and having a fair-price installer. They vary depending where you live.
-Motor & Installation - Expect to pay anywhere from $300 - $500 on this.
-Regulator & Installation - Expect to pay around $250 - $500 on this.
-Window Motor & Regulator with Installation - Pay around $400 to $700.
-Wiring - Cause wiring is a diagnose and fix thing, its mostly labor. Pay anwhere from $100 (If its easy, and only a wire or two needed to be replaced) to $400 (If they have to replace the harness).
As far as a temporary water blocker, you can open the door panel, remove the glass from the regulator, and lift the window to up. Then you have to tape it up. I just put my car in the garage with the window down and drove my other car for a day.
Good Luck and Post Some Pics!