Runs great until warm...? Did you check the air thermal valves? Both under the intake manifold. The big tube one off the throttle body (throttle air control valve?) should close (like a choke) in a few minutes when the engine heats up to block excess air. It's electric (heating element) so if the wire or element is bad it'll stay open The teeny plastic/brass one with two small pneumatic tubes (one to throttle body and one to the transducer that provides vacuum to the EGR valve) is supposed to open when the engine's warm to allow the EGR to work. You can trouble shoot them by plugging the ACV ports when the engine is warm to see if it makes a difference. The other you can just by-pass for a test by hooking the transducer direct to the throttle chamber at any handy port and plugging the tube to the valve. There's that third thermal valve on top of the thermostat housing but that shouldn't do anything unless the engine is overheating or you have AC. I mention it because the lower
port on mine cracked letting excess air into the throttle chamber with resulting bad idle and poor acceleration.