Help Restoring a Yamaha fz250 phazer in south africa

Im a mechanical engineering student who wants to get his hands dirty so I decided to restore a bike and found a phazer for super cheap with a spare engine. Ive always loved the small bore fours and had to get it. Im starting to feel like I bit off more than I can chew with restoring this bike, but I refuse to give up so dont bother telling me this is too ambitious. I have a lot of questions from since Ive started working on this bike and will hopefully regularly post them as I go along. I only work on the bike during uni-holidays

I first want to focus on the motor and have stripped both motors. Both blocks seem to be 2ln's and not 3kr's but I cant find any conclusive evidence. However I have found some random 3kr parts in the engine the bike had.

And thats where it gets strange, the original motor had completely wrecked pistons, after comparing the pistons between two of the bikes I found that the original motor had a crank with a 3kr stamp and 3kr rods/pistons. I know the the rods and pistons are 3kr because when I compared them to the spare motor's rod and pistons, the original rods are longer and the original piston's gudgeon pin hole is closer to the crown. Ill provide a pic. The 3kr crank is wrecked aswell.

 

I had the barrels from the original block measured and the basic measurements I got for each cylinders were: 1. 47.98
2. 47.96 3. 47.95 4. 47.99 these should still be ok right? Ill be able to do more detailed measurements when I get my own micrometer set(almost have enough money). Also how do I remove the the head studs without damaging anything important?
Ill post more questions about this restoration as I go along, feel free to provide any advice if you know of these bikes.