I would not use the longer rod unless you want to tame (slow) the motor down. The longer rod and a spacer will give you less base compression, ( to push the fuel charge up the transfer ports into the combustion area) which makes a big difference coming out of sharp corners, and snap for big bumps or jumps. If the rod kit is 5mm longer, I would pass, if it's only 1 or 2mm longer, you may not notice it as much.
The last CR 125 I modded was a 2001 model for a local expert. The intake track of the rubber carb intake was a lot smaller than the carb. I shaved it out to get a constant size, matched the boost ports to the cases, and roughened all the intake, transfer area's for better atomizing. Cometic used to make special gasket kits with different thickness base gaskets for more or less compression. The bike was able to run with all the other modded cr's, and walk away from the stock CR's.