The skunk 2 intake manifold is hot, I have one, and I was told it's a type-r intake manifold with an improved 4th runner over the type-r one. The ecu you have is very nice. You need it retuned for your aplication. It was tuned for a differnt car with prob a different set up. i have a p28 obd1 ecu with hondata, and with my tuneing it would be worthless in anyone elses car.

Originally i had my vtec set at 4500 rpm, then i put in skunk 2 stage 2 cams and had to change my engagement to 5500 rpms. Originally i was useing a 98 stock obd2 gsr ecu. How much did you pay for that ecu? Do you have a shop that can open it up and look at the chip, and tune it on a dyno for you?