This is what is wrong with the manual choke conversion. The exhaust heated automatic choke has a vacumn passage built in to help pull hot air from the exhaust across the choke coil. The manual conversion does not seal off this vacumn, so you have a constant vacumn leak and this will make your idle problem worse.

Try adjusting your timing this can effect idle speed also.

You need to put a new EGR in, Unless you have done extensive rework to the distributor and changed to a non-EGR carb. Un-pluging the EGR will cause the cylinder temps to go sky high (not to be confused with engine overheating) and burn valves and piston rings.