windstar 96 3.8 how to clear coodes

I have a windstar 96 3.8 I I replaced the engine for a 60000 miles engine. I am getting the same old codes that I got from the old engine when I use the code reader. Is there a way to clear the old codes from the computer and start fresh. I cant pass inspection and I want to see if there is anything wrong with the replaced engine. I am getting the cylinder misfire codes.

Most (if not all) generic code readers have a reset button that will do this.

Otherwise, you can disconnect the battery, turn on the headlights (to drain off residual charge) and wait 15 minutes....then reconnect.

Resetting the codes will leave you with a code P1000 (but not light the CEL).
P1000 indicates that the vehicle has not been through enough drive cycles to complete the OBDII testing process.
It can take some time for this to complete.
Most emission testing places will not pass your vehicle until this code is cleared......through enough driving since the codes were cleared.
This prevents one from clearing their codes on the driveway into the testing place.....and getting tested quick before a code comes up.

Once a failure happens to light the CEL....the code is held in the PCM....keeping the CEL lit for a certain number of "drive cylces"....after the PCM no longer sees the problem.
So.....if the problem is completely solved.....then the CEL will go out on its own after a while.

However, if you still have a problem.....then the CEL will stay lit.
P0171/174 are 2 common codes that would indicate a vaccum leak.....not uncommon after the amount of work that you just did.....as there are lots of vaccum lines....any one of which could be disconnected, or damaged.........causing the vaccum leak......which would give you one or both of these codes.

Update regarding misfire codes.....the CEL will FLASH while this is happening.
Common causes are clogged EGR ports, dirty fuel injectors, plug wires and ignition coil pack.