It doesnt look like a stock engine. Especially with that kind of power! You have nearly 20HP and a good bit of torque more over JDM spec figures! That doesnt happen only with intake/exhaust mods. It looks like there are some more changes in the engine like aftermarket cams or higher compresion ( due to aft. pistons, milled head etc..) in it. This would be a reason why the stock ECU is not delivering enough fuel. Are the HP tq values correct (where there no problems at the dyno)?? Usually if something deosnt work propperly in the PGM-fi system the ECU tends to deliver too much fuel for safety - the opposte to lean. Running lean isnt healthy for the engine as too much oxygen raises the combustion temp. so You should sort it out quickly. Think about tuning the engine with crome/hondata etc You might get better figures out of it