Easy one first. As long as you have no sucking wounds from the swap over (leaks through rtv or wrongly torqued or warped gaskets and baseplates, the normall maladies with all Holley carbs) then the smoking should stop. Some particulates got in the system? There are cleaners avaliable, but go easy with them.
Second item relating to idle jets. According to Pinto engine tuners in the 1970's, the 500 cfm #2300 Holley with a 4412 number was cleaner emissions wise than the 2V 32/36 DGAS and Holley-Weber staged carbs. They could give the SOHC Ford engine over 170 hp, and still remain streetable. All to do with the richer Weber emulsion tubes and fuel staging on the emission cyles. The 16 thou idle circuit was recommended for the four cylinder 2000 cc hop-ups because the ~21 thou (was it?) restrictor was for a 350- 402 small block with 17 inches of water vacuum at idle.
Some where between the stock size and the 16 thou is the ticket. And closer to the stock size because a stock cammed 250 2V will have okay vaccum.
Aussie7Mains and I discussed the issue with non-staged Holleys (350 and 500) being suseptable to poor low speed running if the cam phasing was too much, or the signal was too small in the carb to survive. Holleys have less of a venturi than Autolites, Rochester 2jETS and 2CG's, or Bendix-Stromberg WW 2-bbl carbs. Sometimes, this causes a fuel stand off situation, and this causes the problem. When it happens, a 2 inch spacer can help, but that means bonnet modes in an area were there isn't a lot of space anyway.