GS500 running on one cylinder and noise from engine

[in_shallow_seas]

Hi guys, first post here.
I bought a '99 41k driven GS500 two weeks ago. No major problems with it, only that the engine runs a little lean due to someone boring the silencer.
Well, last week i started hearing a weird noise from the engine at idle. https://photos.app.goo.gl/9gLzkLoy6EwgA5nf6 You can hear it at around 0:08 seconds and after 0:33 in the video. It happens once the engine is warm.
I replaced the oil filter and got myself some new Motul 10W40 fully synthetic oil and thought the sound disappeared but after a while once again I heard the noise.
On Tuesday morning I started the engine to go to work but it only ran on the right cylinder. Once I came home I switched the plugs from one cylinder to another and it started normally. I got myself new plugs and went home.
Then I wanted to check the valve clearances at my parents house. After cooling the engine overnight, using a gauge I found that only one was in spec with 0.05mm clearance and others were under 0.03mm. I reshimmed them so I got 0.05mm on all of them. I used a metric gauge. The engine seemed to run fine after that but on my way home from my parents house I started to hear the noise again.
This morning I left for work and the engine started backfiring and I lost power. Again the bike started running on one cylinder.

Do you think these are symptoms of the same problem or do I have a handful to deal with?

I wanted a GS500 due to its reliability and I'm supposed to hand the bike over to my wife once she gets her learner's license but I don't want her to have to deal with these problems since its her first bike!
Any help would be much appreciated!

[The Buddha]

You have an intake manifold leak or an exhaust leak or something. Doesn't sound like its serious, but find the leak and fix it.
Do the wd40 test for intake, and wiggle and check and exhaust bolts and feel with your hand around where it may be leaking on the exhaust side.
Cool.
Buddha.

[mr72]

I'd do a compression check while you're at it since this is kind of classic symptoms of low compression. Peace of mind kind of thing.

[in_shallow_seas]

Thanks for the replies.
I took out the carbs yesterday and found a 117.5 main jet and 40 pilot. The needle was se to the lowest position. I suspect that the bike had been restricted to 25kw as it says in the registration and someone took the restrictions off without rejetting!
As the exhaust has also been bored I went with a 127.5 main jet and set the needles to the middle position.
Also I found out that one of the vacuum port o rings and pilot screw was missing! The remaining pilot screw didn't have a spring in place...
I cleaned the rest of the carbs and today I will hopefully get it assembled and then I'll do a compression test.

Will report back later.

[in_shallow_seas]

 
Got a new pilot screw and she purrs like new! Did a compression test with somewhere around 10.5kg/cm² with no significant difference between the two cylinders in either wet or dry testing. No backfires since its not lean anymore and plugs looked good.
I'm still just a little worried that I'll hear the knocking sound from the engine sometime soon.
Thanks for the help!

Bonus pic of the bike: