Check out this thread for photos of factory exhaust compared to other aftermarket offerings:
an exhausting tale!!!
Even with full exhaust, there is no need to increase fuel. It's already too rich in factory configuration (+25-30% too much fuel), with slight mid-range lean spot. I have full exhaust, free-flow air-filter and snorkel-delete and Spears Racing still downsized main-jet on dyno-tuning. Along with DynoJet needle which removes even more fuel in high-end, and more importantly, adds fuel in lean mid-range. Clip is at top position on needle.
Yes, check that you have proper thermostat in place.
Thoroughly clean carbs with flossing of all jets and passages. Ultrasonic soaking and micro soda-blasting. Revert back to factory 38 pilot and 98 main jets. Set clip to top position and set pilot screws to 2-1/2 turns out. Leaning out mixtures from current too-rich settings will make bike even more responsive and faster!