Not trying to be rude, but I'd recommend that you stop before you do anything else. You can spend a lot of money by just ordering parts, not to mention if you order the wrong parts and the distributor won't take them back. When you say that it was smoking from everywhere, it scares me. That's never, ever, EVER a good thing.
If you Google Mikuni jets, you'll find all kinds of places that sell jets to fit a Mikuni. That doesn't mean that they're genuine Mikuni. I'd consider that jet kit a bag of emergency only parts. Go to a Yamaha dealership and tell them that you want 260-300 main jets.
First order of business is to post a picture of the bore and measure it. Wait on someone to tell you whether you need it to be bored or not.
Don't order a gasket kit from anything other than OEM Yamaha or Cometic (like Blaaster said). If you shattered, broke, or did whatever to the piston, you need to split the cases. Not doing so will result in endless rebuilds until that is done. Aluminum destroys aluminum, so if pieces of your piston are in the bottom of your cases, you'll eat pistons until it's all out (which could be many, many rebuilds along the way).
I'd also recommend that you post pictures of the dome because detonation damage is possible.
The short answer is to send the cylinder, head, and a few hundred bucks to KOR and let it be his problem. He'll set you up pretty well and you don't have any guess work there. Next, split the cases and clean the crankcase. Replace any bearings that don't look brand new and replace all seals while you have it apart. Reassemble the bottom end as per the manual (which is on this site). Do a leak down test, install a 290 or 300 main jet, needle in middle position, screw at 1.5 turns out, install a UNI or OEM filter WITH OIL, check all of your electrical (again, reference the manual), run heat cycles, do a break-in (KOR will recommend both the heat cycles and break in procedures if you sent the cylinder to him), do another leak down test, pug chop, adjust jetting as necessary, plug chop to confirm. With the exception of sending it to KOR, none of this is optional. If you don't follow these recommendations, which are going to be the same as those of others, you are destined to go through this again.
The price of doing a proper rebuild is roughly what it costs to do a hack of a build twice. Do it right and postpone the next rebuild by a considerable amount of time.