I have a 2000 model civic, and, my problem is that its due for an overhaul. its a VTi model (i'm from the Philippines) and i was just wondering if putting back my stock pistons (engine code is for D16y6/y8 counterpart here) would return my ride to its stock HP since my ecu was replaced with a d15 ECU instead of the original one, since i got it from a used car dealer. Will replacing the pistons back to the original set solve this, or do I also have to replace my ECU to the original one. anyone who could shed some light regarding this matter would be of great help.
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No, displacement is determined by the crank not the pistons. Try to find the proper ECU.

ok, i'll try to check the crank later or in the next few days. but what if it's stock set? will the ecu read it as a 1500 or a 1600?

The ECU is permanently set for the type of engine. If you have a 1600 cc bottom end, it's 1600 cc. It doesn't run right because the ECU looks at the rpm and is only putting in enough fuel for 1500 cc. You need the matching ECU.

ok, thanks for the help. my next question: After i'm done doing the overhaul, i plan to swap my transmission into manual, problem is, it's from a non-VTEC model. I plan to go with the swap, and get the ECU of the non-VTEC engine as well. will this affect my engine? its a VTEC model. Cause if it will, i'd rather do a full engine swap together with the transmission. thanks again!

the transmission from it will work, but you'll need a manual ecu that corresponds to your head (VTEC)

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Lol, you cant have Vtec without a Vtec ECU.

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95 Civic CX Boosted 9psi
JDM D15B VTEC (LSD Tranny)
TE04H Turbo (14B)
Magnaflow Cat-Back Exhaust
460 cc Rx7 injectors
Front Mount IC

In order for your VTEC to work, you need the ECU to be compatible with VTEC engine

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Thank you so much for the help guys! my mind's getting clearer. i'm doing the overhaul right now, and my hunch was right. 1600cc displacement, (just by looking at the piston codes alone) and a ##$%^%#@ 1500 ecu. im asking help from my bro to look for the proper ECU and the tranny i need too. hopefully this project of mine would bring my car would be back to life. thank you, thank you, thank you!