On my 1999 integra there is a plastic container with some hoses going into it that sits under the inside corner of the battery, about six inches down. From (over)filling the battery, acid had dripped down and eaten a hole in the top of the plastic container. That hole was causing the check engine light to come on.
I don't know to this day what the container is for. I cut out a little triangle of stiff plastic, gobbed some adhesive on there and covered up the hole nice and air-tight. Let it dry for a day, unhooked the battery to re-set the light and fired it back up. That was two weeks ago and the CE light has not come back on since.
oneputtster