97 Taurus 3.0 w/auto transmission

I have a 97 Taurus w/ automatic transmission. The car has a 98 engine however. I recently acquired this car from a friend. He put the 98 engine in the car since the last engine was basically on its last leg so to speak. After installing the engine, he drove the car for a while without any problems. It started, ran, and shifted fine. However, a couple of months ago when he still owned the car, he said it began burning fuel very rich and about the same time the speedometer quit and the transmission would not shift out of first gear. The car runs rough at an idle and you can hear the idle as it is very inconsistant. If I rev up the engine it will spit and sputter quite a bit. I'm sure this is due to the fuel problem. As I said, I recently got this car. My friend was tired of trying to figure out the problem so he just got a new car and gave this one to me. There is a check engine light which I plan to get the codes for very soon. Nevertheless, I am wondering if the fuel problem, speedometer problem, and failure to shift are all related since they began around the same time. The V.S.S has already been replaced so that didn't solve the speedometer or shifting problem. Furthermore, I am aware the transmission is fine. Whenever I start the car, I must drop the transmission into 1st and drive up the street until I reach 3500 RPM and then I can shift into overdrive and from that point on the car will shift on its own. I can then stop at a light or stop sign and when I take off the transmission will shift out of 1st gear on its own. I only have to do that after I first start the car. The car has been taken to a shop and the mechanics determined nothing mechanical is wrong and therefore it must be electrical. My question is, given your automotive experience, do you believe the problem might be the P.C.M. Or another problem? I've worked on my own cars many, many times but I've never had an electrical problem before. Upon researching the powertrain control module for this car, I've found that it does control the transmissions shifting and the fuel mixture. It seems very rare that a P.C.M. Goes bad on a car but in your honest opinion do you believe that might be the cause for this trouble? I would appreciate any input you can offer. Thank you.