Rods where shot.. As in no good

so I found out when all pulled apart. The motor had been rebuilt sometime in the first few yrs(pre 50,000km) when I bought it 8yrs ago.
I've just bought new std rods but with the extra weight of the JE pistons I had decided to balance it all up again and knife edge the crank while at it.
The guy who has the head at present doin the work on the valves has made me aware the yamaha cranks are pretty good as I found with mine in excellent condition.
The thing he made me aware of is the caps on rods may stretch a little at that point from over revving or if you miss a gear. He also told me that it's always best to try to keep within the middle of your tollerences on the bearing shells so stick with the numbering/colour code as sometimes when you start the bike after a resting it a few minutes some yamahas he has works on suffer moreso than the trx is is sounds a little tight on turning it over with the starter. This is from the alloy case cooling faster and shrinking more than the heavier steel crank which holds it heat a little longer.
Once the head is back and pistons rebalanced I'll take the piston, head ,valves n springs off to get ceramic coated.
I've been questioning the different design on the STD TRX pistons and rings compared to the JE ones and found the answers there too.
The std trx pistons dont have a full skirt like the JE pistons . The stock piston also has curved rings and all this was factored in for the piston rock so as it reaches top of its stroke and about to pull down the piston rocks a little and the curved ring allows for this and the skirt design stops piston wear while this happens.
But with the square rings on the JE piston this rock is actually taken up in the ring groove on the piston rocking up and down in the groove and allowing to keep the square edge of the ring flat against the bore so the skirt doesnt become an issue. I've also learnt that the seal against the piston and the top ring is actually improved here also because of this.
I have looked into coils and programmable timing units too so I'm going down the route of less friction, less heat ,less wear and all those little things just adding up to the useable gains .
I'll be using a set up with a couple of bungs drilled/ welded on the pipes so when running we have O2 sensors in there and a meter mounted on the tripple trees. A cam set up to record the meter/taco/ throttle as I'm off for a ride and get the carb's running to their optimum.. So I would say by xmas I hope to be up n running. Suspension sorted and 320mm brake disc set up.
I'll stick with the std swingarm and 170 rear tyre for now and get a feel on things.
So thats where I'm at and what I'm up to.
AS FOR THE PISTONS ,THESE PHOTOS WILL GIVE YOU BIT OF AN IDEA OF THE DIFFERENCE. ALSO NOTE THE OIL HOLES UNDER THE YAMAHA PISTONS TO AID IN COOLING AND LUBRICATION OF THE PIN. THESE ARE FED BY THE HOLES IN THE PISTON WHERE THE OIL RINGS SIT IN THE GROOVE. ON THE JE PISTON THERE IS AN OIL HOLE THAT FEEDS THE SEMICIRCULAR GROOVE ON TOP SECTION OF WHERE THE GUDEON PIN SITS. THERE IS ANOTHER SEMICIRCULAR GROOVE OFFSET AT THE BOTTOM TO RELEASE THE OIL AFTER LUBRICATING THE PIN ALSO FED BY THE OIL RINGS.
