Yamaha Yx600 radian 1988

Hi,everyone my name is brad. I'm new to forums all together. I purchased a 1988 Yamaha yx600 radian 8 months ago. I bought it for 150. It was complete other than battery an had been sitting for 3yrs. The guy I bought it from said it had run fine until he decided to clean the carbs. I got new battery checked a few odds an ends. Then turned it over. It run but very rough an carb 2 was spitting fuel into the air box. I rebuilt the carbs changed plugs added pods an a 120 main jet
. That may be a little much also they sent the small jets an it had the large round jets. I went ahead an used them cause he had really messed up one of the old ones an the washer was missing. Oh did I mention this is my first street bike also first I've ever owned ,worked on myself etc. I bench synced the carbs. All was fine for a while until I messed with adjustment for clutch (lower). Replaced clutch cable lubricated all others an any other general maintenance. I purchased a clymer repair manual. But now it has that knock timing chain slap noise at idle mostly. It's not bad but very noticeable to me an I don't want to hurt anything. Early in the repair process when dealing with carb 2 the header pipe was not getting hot an acted as if running on 3 cylinders. Several eliminations till that was fixed. But even then it didn't have this noise. But now I noticed it is now taking a long time for 4 to heat up an it's not much when it does an 123 are good. I assume that may be the source of where my noise is coming from partially anyways. It is mainly coming from the clutch area but pulling the clutch lever doesn't affect the noise. I was thinking of the dowel pin but ??? Checked coil, plug wire , boot, fire is good. Have not been back inside of carbs but did check bench sink again but no luck with that. Can anyone please help??? Also I can't find a happy middle for the clutch either to hard of a shift an kills it from a stand still or slips in high gear. Also if it helps I have not checked valve clearance yet. Thank u for any help

 

You'll get a lot of input here I'm sure, but yes, if pipe doesn't get hot, that cylinder isn't running or not running much.
first thing's first. Check compression. Take all of the plugs out and check each cylinder. You're hoping for fairly even compression. Next would be carbs and I'll give you a couple of links to read through:

https://www.xjbikes.com/forums/threads/the-information-overload-hour.27544/
https://www.xjbikes.com/forums/threads/in-the-church-of-clean.14692/

If you're bored after reading those, get back to us!