Bottom end noise???

I recently had to rebuild my top end as I duated it. Seemed to be coming thru the intake boots. I did Oem Pistons/cylinder/rebuilt head. Oil was fairly dirty so I flushed it 3 times wit the old filter and then last flush I changed filter and put polaris oil. Fired it up ran great. Put about 5 miles on it. Ran great. Didn’t push it. Then all ov a sudden I let off the throttle and it died. Started it up. Running good. Started going again. Started making a rattle/clunking type noise stalled again. Checked oil. Looked good. Started again. Won’t stall anymore but idles fine but when u rev it up in p/n or even moving it sounds like bottom end. Took clutch cover off. I can hear the normal clutch rattle but off idle it sounds rough. I guess my question is 1- are bottom ends common one the 900xp and 2- how can I tell if the oil pump is working and supplying oil to the crank etc? I’m waiting for a puller to come in so I can pull primary and hear it better.