When I had to replace my CCT the chain sounded like a bunch of rocks pinging the inside, and also like something was vibrating right on top of the engine. According to the PO, he said he'd hear it sometimes and then one day it was there. Could be you're really noticing it now because you're listening for it if that makes sense. Try replacing it and see if that helps. You could always sell it if it doesn't. Or keep it for your new engine if you go that route

 

Update, all cylinders are for sure firing by the damn that header tube is hot test. I heard it's best to just get an ape because sometimes the chain is stretched to where the regular one won't work, mine is at the very end of its extension, I can barely even turn it in at all from what I can tell, seems to quiet a hair when I do, might try a better screwdriver and see if that does anything more. When I turn it out even like a quarter turn it gets extremely loud from the same area, so might be onto something.

 

Update. Took it to a shop and they confirmed that it is NOT the cam chain tensioner. They said that it is probably rod knock, so I'm not sure it would be worth fixing since I have shifting issues from first to second anyways since I owned the bike. It has quieted up since riding the bike more and getting on it. When I do get on it it somewhat goes away, maybe due to higher oil pressure. Right now my thoughts are to go with 20w 50 and see if the boost in pressure helps much or not. I am not going to take the jug off or split the cases. If it comes to that it will be new motor time and I will get to this one when I have time over winter just so I know what happened and maybe to sell the good parts in it.

 

wow that sucks to hear but thats what i was thinking it was.

 

Could it possibly be a gear in the transmission like an idler gear of sorts that would always spin and that's what ticks?

 

The suspected rod knock is a very likely candidate for what happened with the drain plug. You cant run a motor without oil and just fill er up and expect it to continue to operate without fault.
The funny thing about honda's motors is that when/if they develop major internal problems, they will continue to run for long periods of time. Much longer than other manufacturer's motors with damage. But having a rod knock and continuing to ride your bike at its full potential is not a good idea.
If you have to use it for work/school, i would recommend to stay out of the high RPM's, cause one day you may trade a rod knock for a rod thru the case. Anyhow, what ever you decide, be safe and good luck.

 

Thanks everyone for the advice, I found a good used motor for probably what it would cost for a rebuild when all is said and done, motor is only 500 and comes with carbs, plus it's a 98, so win.