Most likely the reason your car overheated, given your particular situation, where it only overheated as soon as u put new ECU in...is prob because of the ECU's fuel curves and more importantly the ignition timing. If u ran P28 on a D16Z6, then it should be ok, but maybe the ignition timing is set incorrectly (distributor), and when u try and use the P28 with VTEC, it changes the timing, for worse, making the engine overheat...
Plus I'm not sure how good it is to run a P06 with a D16Z6 motor... Can't say that damage was done, but I'm unsure...
Did u try and put in P28 again and see if it overheated??
is it ONLY when the P28 is in, that it overheats??