Loud clunking noise when bike is running

SOURCE: 98 fatboy engine noise.

Harley's do run hot, anywhere from 220 to 240 normally, and a little hotter this time of year. I suggest running a straight weight oil, and a little heavier weight in the summer. I use Valvoline VR-1 30 weight most of the year, and 50 or 60 weight in the hot summer, and I use Lucas 20w50 primary/trans for the primary and tranny. I don't bother with the extremely high prices of the HD oils. For the whining noise, you need to determine which side of the engine it's coming from. Whining will almost always be in the bottom end. There's nothing in the top end that should whine, and if there is whining from the top, it's usually an air leak around the carb. Start by checking the fluid levels in the tranny, and primary. These are the two most common areas to pick up a whining noise. If it's coming from the left, it's going to be in the primary, and usually this is caused by low fluid levels. From the right, it's going to be either the tranny, low fluid, or the oil pump. The oil pump is a gear type system. If you're running a light weight oil, say a 10w40 or HD 20w50, when the engine heats up and the oil thins, it can cause the oil pump gears to whine a bit, especially in the summer heat. So, check the fluid levels, if they check good, then change the oil, since the summer is coming to an end, go with a straight 30 weight. This should clear up the whining noise. If it doesn't, get back to me with the exact location the noise is coming from, and we'll go to the next level of diagnosing the whine, but I believe that this will cure it.

SOURCE: LOUD TICKING NOISE IN ENGINE AFTER INTAKE REPAIR

How long have you ran the engine ? I know that they will run rough and sometimes make strange noises for a few secounds or a little bit untill everything get oiled up again. I would make sure all the push rods are back in the right place and that all the lifters are tight.

SOURCE: oil light flashing/engine knocking

you are abouot to lose the motor,,,,you have a rod knocking when you start it up and an oil pump wont help it been there done that all it does it make it worse

SOURCE: engine knocking problem,no start even with kick,kick becomes free

This was the same problem what I had with my New Unicorn. I approached the Service Center through Honda customer care, and now got a solution which is not bad. I could meet with a senior service manager and technician there and they really supported me solving this problem. I will brief out the findings and solution here:
Findings:-Engine heating up than normal, Exhaust valve misbehaves at this extreme condition. Air block is happening at the time of exhaust stroke inside the engine.
Solution:-Engine was overheating than normal because of bad/changed valve clearance and improper oil pumping inside the engine. They corrected valve clearance for now and replaced entire oil pump unit inside engine. Replaced rubber mounts on top of both valves. Replaced the clutch lift plate because of bent formed after trying so many kick starts while piston movement was interrupted due to air block.

SOURCE: The bike will not go into neutral gear when engine running

my husqvarna sm450r does exactly the same thing and my girlfriends yam virago is just as bad, i think some bikes are just too tight, rocking works or try finding neutral as you roll to a stop, on both our bikes it does the trick... nothing worse than trying to find neutral with your hand lol

Dude 48 bikes, impressive! im up to 9 in 20 months since my Ls :)