1993 Mercury Tracer erratic shifting

I just bought this car and the check engine light came on. I tried to check the codes but don't understand them the light flashes weakly once then 3 times and three times and it flashes more and seems to have a single digit left over at the end, and it speeds up from 2 seconds at first to less then one second. When I first started working on it there were only ones two and threes(33, 13) now is shows four and fives.(54 or 45) I put in new spark plugs and changed wires. Egr, and vacuum controller for the egr, from an other car. I checked the line to the egr and the side pipe to the egr modulation sensor. Some times, The car will shift rough and require a lot of rpms and some times it will drop to first gear and coast until revved up (free wheeling). It seems the transmission had been replaced and the computer accessed. I have parts from a 1994 but don't know where to start. Also the book said the timing is controlled by a cam ramp sensor but I don't know where it might be.