My son bought his first vehicle and it is a '99 Dak Sport with a 3.9L V6 manual transmission. It ran ok but had a misfire on cyl 4 (P0304). We did a leak down test and found that cyl 4 had a huge leak in the exhaust side. Removed the heads and found a valve that was not seating. We went ahead and replaced both heads. Put everything back together and took it for a test drive. Ran ok but not smooth. I didn't bleed the coolant system well and their was air in it. Took it for a drive and in less than 5 minutes it began to overheat. Shut it down immediately, let it cool and finished topping off the coolant system. Drove home and still ran a little rough. Replaced IAC, coolant temp sensor, cap, rotor, wires, and plugs. Now it runs like garbage. Started getting a P1391 code so I replaced the cam sensor and crank sensor. Now I'm getting P0340 and it still runs like garbage. I did a continuity check on all the wires from the pigtails to the PCM plug and they are good. Never disturbed the distributor during the repair. What do I do now?