Welcome aboard! Although you may have a lot of work in front of you, YJs are a lot easier to work on than modern cars. 
Do you have any pictures on-line. If you do post a link to them so we can see what you got.
1rst thing: don't open a magazine and want to buy everything. That's very hard NOT to do.
2nd thing: set a plan (which will come as you learn more about what you got and the issues may have)
3rd thing: spend wisely. That way you don't get into upgrading the same parts multiple times because you changed your plan.
2x on john, 1st fix everything to make it safe and fun. Remember, lift/gears/locker/tires will probably cost more than you paid for the jeep. Plan on adding skds , rockers bumpers first.
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If you can find one, the TSM (technical service manual) would be better. But the Chiltons will have most of what you need for the more basic stuff. TSM would have what the Chilton has plus total rebuild information.
Welcome and congrats on getting your Jeep. There's a lot of good, helpful people here that can get you through just about anything Jeep related. I'm also a YJ guy and agree with the above posted advice. Get your Jeep road worthy and reliable and then come up with a plan on how you want to use it. The Chilton/Haynes manuals are good sources for repair help. If you're not already on Jeep Forum, start perusing the site... especially the YJ Tech page (http://www.jeepforum.com/forum/f12/). Search for the YJ FSM there... someone has it in PDF form, free to all.
....and post up pics of your Jeep! 
Welcome 
Welcome!
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welcome! I have the manuals for my jeep, but usually end up using youtube or other online videos
Welcome! Through this site I have learned a lot about my Jeep. Lots of great people and information here.
Questions about the problems found in the Jeep have been moved to Jeep Talk so they will get more attention.
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