I have a 99 accord sedan v6 vtec that has surging/ flicking lights in the inside and in head lights on car. It’s burning my gas fast and has poor performance etc pretty much all the symptoms of a bad ecm/pcm. Can we crank and drive after sitting for a while but if I drive it and the shut it off it takes a while for it to start back up . And main relay gets warm but I checked and replaced that already .I have some CEL codes that won’t go away even after replacing the parts.I took it to Honda to get a diagnostic done. They said my engine over heating but I see no smoke nor is my gauge reading hot. And my car doesn’t shut of or stall. Honda said I need to replace engine And that my thermostat bad possibly something is not allowing the engine to cool or my head gasket bad ...help .

These are the codes I have but have been replaced

map sensor
tps sensor
iat sensor
maf sensor

was a egr sensor but it went away after replaced

and now it say automatic transaxle after I got trans rebuilt

they did do the interlock recall

 

a faulty alternator can cause some of these issues, especially the light flickering/pulsing. it may be worthwhile to have it tested. if found bad and you decide it's worth the expense to replace then go back and check on the other issues to see if any have been eliminated.

 

For the overheating possibility, you can do a flush to see if there might be blockage and remove the thermostat for now so it's always flowing to see if there is an improvement.. The flickering also sounds like an alternator to me. But all those errors together starts to sound like an ECU issue causing everything to go haywire.