Clunking into gear is a clutch drag issue. If not addressed in a timely fashion trans engagement dogs, and shifter mechanism wear and damage follows.
Clutch drag can be poor adjustment, warped clutch plates, wrong or worn out oil, clutch plates overheating, broken shifter rod, etc.
Are all the headers getting hot? #3 spark doesn't look like it is firing. Best to find out why that is. Dead cylinders WILL pump out oil.
What is the status of the routine 3000 mile tine up schedule? That and a carb vacuum sync can make a huge difference in the clack at idle. Uneven firing pulses change the crank rotation speed causing the big gears to alternate gear face contact. Clack, clack, clack.
White smoke from the breather is usually water vapor. Has the engine reached operating temperature and held there for 20 minutes to evaporae all the water in the crankcase?
From the Honda manual instructions, oil level is checked with bike upright and level, with the dipstick threads NOT engaged.
The broken stud can be extracted and then replaced. I don't know about your mechanical prowess, so it might be prudent to have that work done for you by a qualified mechanic or machinist, as there is opportunity to damage the head.
For the valve inspection covers use ONLY a 6 point socket on those for removal. Or, be prepared to buy replacements.
