Yamaha sr 125 engine knocking vs normal sound

This is my sr 125 bike. At the beginning of this video you can clearly hear that the engine has a bad sound. I replaced the engine ( cheaper this way) with '99 model (same 10F code) but I kept the old electrical wiring harness and flywheel and stator because the 99 model is not compatible with the old version, magneto plug to cdi was different, ( my bike was made in 96). Anyway the new engine as you can hear has a different sound (has only 10800 km).
Feel free to ask if you have any questions regarding the engine swap.