99 WR400 mods help

This bike has sat for a year or two, then fixed the broken kick starter and case. I did the throttle stop mod, exhaust cam timing mod, removed the airbox lid and baffle. The bike also has an on-road conversion kit. After doing the mods and trying to start it, I took apart the bottom part of the carb and cleaned out the jets w/ carb cleaner (especially the idle circuits). Now I have to turn in the idle stop screw to get it to idle (I think it's pretty close to idle rpm's???) and the header pipe is red when riding it for 2-3 minutes. I rechecked the cam/crankshaft timing and the throttle position sensor, all were good. Is this normal? The article said I didn't need to rejet the carb. I'm in the desert at 3000 ft elevation.

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