93 Escort Electrical/Engine Problems

1993 Ford Escort 1.9L AT A/C 155,500 miles
When I got this car it had a broke timing belt and the battery had been hooked up backwards. Also the fan has been wired to run whenever the eng is running. I have replaced the timing belt, alternater, 100a main fuse, head gasket and bolts, t/stat and #2 inj. The fan is still wired to run when eng does. When the following are disconnected it has no effect on the engine: TPS or Air Charge Temp Sensor, disconnecting the MAF Sensor causes the eng to shut off. For some reason when I try to retrieve the eng codes it does not work like the manual says. I have checked every thing I possibly can using a Haynes Manual and this is what I have: At first startup the RPM's surge about 300-500 and as it warms up it stops surging ALL MOST, still has a very slight surge. It idles rough, like intermittent firing. I can remove the #2 (new inj) plug wire and can not notice any change in eng, I have power to the inj and it ohm's out within specs. The TPS has 5.05 volts going to it. Is this normal or should it have 12v? When the eng is switched off it keeps running for abt 3 seconds before it stops, and the tach goes all the way to the high side of the gauge. When the eng is restarted the tach does not move until you rev the eng up to abt 2,000. Any help would greatfully be appreciated. Thank you. :(