OK
STUD - you only need to replace the stud that is missing.......let me know I may have one for you...
TOP END - I think everyone will recommend Wiseco Pistons...you can get a top end kit from a site sponsor for a good deal.....includes
pistons, rings, circlips, wrist pin bearings, new rings...everything u need for your top end......
Cool Head - Running cooler is not what u really gain from this.....you get to change the domes at the top of the engine above the pistons.....this increases the compression of the engine giving it a little more power.....a little! It is a good mod....but you dont need to do this.....you can have your stock head machined as well pretty cheap.....and this will do the same to your compression without interchangable domes...
STROKER - yes you can install a stroker kit like a car....a 4mm stroker kit is the most feasable.....it gives you 2 mm more of stroke on each side increasing compression and power significantly....This is a lot more costly......it is a whole new crank.....they have both a short rod 110 and long rod 115 option......There are many posts on building these....just do a search
POWER - A port job of your cylinders will be a good option especially if you have the engine apart......it is a little pricey as well to do this but worth it....really opens the bike up.....call Brandon @ Wildcard racing or JEFF at F.A.S.T. racing they do excellent work and will have your top end parts!
You can get an adjustable timing plate and increase the timing which will get a squeak of power........the cool head with the different domes will increase power......you will need to run race gas at a certain dome size......please search for cool head posts regarding the benefits/disadvantages
Check your cylinders to make sure your bore is still within spec before ordering your top end kit!!!!!! YOu can take them to a local shop and just have them mic'd out.
Thats all i got for now....