Someone told me that your always going to have an error message when you do the det swap. Something to do with the EGR valve and a flywheel sensor. Is there any way to clear these to pass emissions? And if there isn't I don't need to worry about a rear O2 sensor right? My reasoning for this is if I'm already going to have the check engine light on, and it won't affect how the car performs if the rear O2 is there or not. Then why not just leave it out?
Any help would be greatly appreciated.

well if you leave the rear o2 in and get a resistor in the egr temp sensor or somewhere in the egr sensors. i think ive read something like that by reading old treads

Can anyone else help out here?

It depends on the year of your car. OBD 1 or OBD2. if it is 98 and later then it has to be tested as an obd2. before this you can still test the car at the station using the OBD 1 testing meathods.
In order to reuse your stock smog equipment you are going to have to go to Jim Wolf to get the ECU reprogramed. I do not believe the JDM ECU's are set up to use the stock smog equipment. You will probably have to do some fine tuning with an SAFC so that it will run well enough to pass smog. JWT has a tendency to run slightly rich.

The EGR code will not trip if you leave everything plugged in, and the flywheel code will not trip if you have the correct flywheel, or an OBD 1 car.