You can't just close it back up once you've opened it!! You'll have to re-seal the case halves. And, if you've gone through the trouble of splitting the case halves....you might as well put some new bottom end bearings in while you're down there (especially considering what happened to the piston!). Even if the bearings looked fine (which in your case would be surprising), you might as well replace the bearings you can while you're in there.
Now, if it started and ran in this condition....like I said before, you MAY be able to get away without messing with the bottom end. It is definitely unlikely and I don't think anyone here, myself included, could in good conscience tell you to just forget it and put the top end back together. If you did it that way, the chances of the bottom end failing in the near future would be high....but you're the one who's closest to the quad and making the observations, so ultimately you've got to make the call. However, it is potentially a possibility that if you made sure nothing was down in the crank (I'm using bottom end and crank(case) interchangeably here) and then just threw the top end back together that you could end up being fine.
Tools: flywheel puller, wooden work bench (or you can make a cradle out of 2x4s for the motor to sit in) good quality screwdrivers (I hate how yamaha uses phillips heads!), an impact driver (for those hard to remove screws. The type of impact driver where you hit the back with a hammer and it turns the screw), shop manual, lots of rags, camera, cardboard to lay out all the screws you'll be removing (like said above, this is not the type of job you just throw all the bolts into a can and remember where they go later), rubber mallet, Some use an actual case splitter....although I've been successful using a rubber mallet, lots of care, and wooden wedges for prying the case apart. Oh, and a torque wrench!!
That's what I can think of at the moment. Oh, you'll want a good clean dedicated work space. If you don't have a shed or barn or garage to do this in, you can pull the motor outside and work on the motor in a basement shop or (don't tell your mother) in the kitchen!! CAUTION: mothers usually aren't to thrilled to come home and find a motor being taken apart on the kitchen counter!!
The only thing that I'm worried about walking you through this is breaking bolts off in the motor. I've done it a million times. Luckily, I learned how to break the bolts off on side case covers and such, where removing the bolt wasn't so bad. If you break a bolt that holds the cases together, that wouldn't be good!! There is a feel to tightening the bolts..sometimes before there all the way tight they'll bind up and can break. IMO, it takes a few times of breaking these bolts to get the feel for when they're gonna break and know when to back off....but hopefully you won't run into this problem.