Honda Fourtrax 300 troubles

So I’m new here but you guys have helped me a lot just by reading. But I’ve got some issues that have me stumped. This 99 Honda Fourtrax was my first wheeler ever. Ran excellent for a year but then found out I was taught incorrectly on putting the oil filter in. Ran for a YEAR of daily riding and heavy abuse in the mud. FINALLY she started ticking bad. Didn’t know this was a very bad sign so I kept riding for probably another 6 months and finally one of my buddies pointed it out. Assuming top end is fried and need a complete rebuild? Still starts up and runs beautifully besides the major power loss in the higher gears. And then I drowned her finally after two years of playing in deep mud and ponds. Air box was full drained it started her up (probably my worst decision) and she started right up but died when I hit the throttle. Got towed out by a buddy replaced the carb entirely. Changed the oil and filter twice. Checked it for a week and stayed Golden. Well now she’s milky and the only reason I realized was because I had vapor looking smoke rolling out the crankcase vent line. Stopped riding it once this happened. What caused this? I didn’t get all the water out ? I pulled the spark plug and turned her over multiple times and hardly
Any water came out. Also I have pure white oil on the inside of my valve cover? Appreciate if even one person reads and helps me out with my Novel of misery lol