2002 Expedition Missing Intermittently

I have a 2002 Expedition that has 147,000 miles on it. I had the transmission replaced with a Jasper transmission when the stock transmission failed. Since then it has been running rough when cold and missing intermittently at idle speeds in or out of gear as well as missing at highway speeds. It is most noticeable when first started each morning. I have had the plenum cleaned, fuel filter and fuel pump replaced and it still misses. I have removed each spark plug and dryed out any moisture in the coil connections. Any ideas?