I assume you are using the Civic STD engine and chassis harnesses which have been converted from DPFI to MPFI - is this correct?
Do you have the CRX HF firewall mounted control box which contains two components necessary to control the EGR system?
Be aware that the Factory Honda ECU pinout numbers on your diagrams are different from what you will see just about anywhere you look for ECU pinouts - for some unknown reason, someone decided to change the numbers and then this got published everywhere, even in some manuals purported to be "Factory Manuals". The difference is in the numbering system - Honda numbered the ECU pins on the top row of the connectors consecutively such as A1, A2, A3, A4, A5, A6, A7, A8 and then continued the numbers consecutively on the bottom row such as A9, A10, A11, A12, A13, A14, A15, A16, A17 - the other numbering that you will see most places has ODD numbers (A1, A3, A5, thru A17 on the top row - there is no A9) and EVEN numbers ( A2, A4, thru A18) on the bottom row - just something to keep in mind so you don't get confused - in fact, if you look at the connectors they have the Factory numbers right on the connectors