First of all the tool you're asking about is called a wire saw and is pretty much a specialist tool that you can't pick up at any hardware store. I have bought them from matco, snap on, mac etc, but their quality is poor as they're better at making mechanics tools, and a windshield is something a mechanic shouldn't be mucking with...they should leave it to guys like me that have the training and certification to do so.
Second...a windshield is something that you should not be messing with. An improperly installed windshield can kill you, your family and anyone near the vehicle if you're involved in an
accident.
Third the black goo you're talking about is Butyl and is illegal in many places to use as windshield retention device. The only places that it is used anymore is in large semi's where the windshield isn't an integral part of the frame. Just because some of the local auto stores sell a windshield installation kit does not mean that it is legal to use...check your laws...and if you use butyl stay away from me and my family because your vehicle is a death trap...especially if you're offroad with it.
A properly installed windshield will be installed with a urethane system. This systems generally consists of a number of different primers, activators and the urethane. If one of these is missing it can cause the windshield to release, which is not a pretty sight (trust me I've seen the aftermath). The urethane used in windshields is extremly tough...it's like a giant rubber band on steroids that sticks to the glass and pinchweld like a M.F.
It is worth the money to get a good quality windshield and have it installed by a certified installer at a reputable shop. Don't go with the cheapest guy out there either...I can guarantee that he's skipping steps somewhere, which in the end will compromise YOUR SAFETY. If he's claiming to use OEM glass and is fairly cheaper than the other shops out there, he's cutting corners somewhere....he has to be or else he's not making any money, and is someone you should not trust your XJ with.
I recommend that you spend the money on an OEM windshield...they are properly designed, fit better and are a safer piece of glass. Aftermarket glass manufactures only adhear to the sheer basic of federal saftey standards, which just aren't enough for the vehicles on the road today. (trust me I have some horror stories when it comes to aftermarket glass) OEM glass will meet the vehicle manufactures standards which are higher than that of the government. Why is this? becuase safety is generally what sells a car...the safer it is generally the better it sells.
Just my $0.02, but when it comes to a windshield what you don't know can kill you. Also a boneyard windshield is generally trashed so badly, and is usually so contaminated that you can't get a good bond to it with the new urethane. This is such a problem and is dangerous enough to the customer that we refuse to install any boneyard windshields.
Hope I at least get you think twice before you compromise your safety on your next trip to the boneyard.
If you're interested drop me a PM and I might know of a good shop in your area, I can promise that they won't be the cheapest, but they'll do it right, and take care of you.
Matt