Bog out at low rpms

[Floop14]

After replacing intake valves, new air filter, carb clean and an engine rebuild, my 04 gs500 is back up and running and sitting at 1200-1300 idle. It will idle fine, but the moment the clutch is let out it starts to die and bog out. When given gas in neutral, from 2-4000rpm the engine has a flat spot where it sputters and refuses to make power. It has to rev to 4-5000 to start moving down the road. Once at speed it will keep running like a dream. I have the mixture screws at 2 turns out but tested at different amounts between 1.5 and 3.5 turns to see if anything changed. Same issue persists.
I noticed the right cylinder is getting hotter faster than the left. I'm pretty sure this has something to do with the problem. The left cylinder wasn't firing on startup when it was first put back together. After some carb love, both cylinders are firing right at start up. A slight popping is coming from the exhaust, but with the carb tweaking it got 10x better. The popping still won't go away though.  Any ideas what might be going on? Besides carb tuning, I'm not sure where else the issue could stem from. Any help is greatly appreciated.

[grader]

try going up a size on the pilots from 17.5 stock to a size 20. my 04 did the same thing as its lean from the factory.

[Floop14]

I checked the rejetting wiki and it looks like an up size to 20 doesn't require a new filter. Ordering the jet and hoping it solves the problem.

[lucas]

Perhaps the left cylinder is not firing on every revolution.  I think I heard a faulty or weak ground connection from the CDI can cause weak spark on the left cylinder.