I have a 2000 civic ex with a motor swap and now has a 96-98 vtec motor in it, the only thing we swapped over was the motor and the harness but the car won't start. Any suggestions on what it could be?

 

Yup... rookie mistake. You cannot use the '98 engine harness in your '00 Civic EX. Move the '00 engine harness AND the distributor over to the '98 engine and you should be fine... except for the coolant temp/idle up valve. Otherwise, it should crank and run just fine.