I have this same problem. On my X, which coincidentally (or not) is also an '01 5-speed 3.0, it's intermittent. Some days I have no codes and the CEL stays off for long periods of time. Some days I get one or two codes for O2 sensor heater circuit (usually bank 2) and it drives fine. Yesterday the light was off, then I was sitting at a stop light and it started to idle rough, and the CEL came on immediately. I pulled over, scanned it, and it came back with three codes for O2 sensor (one that said no input detected from O2 sensor), and two misfire codes. Turned it off, started it back up, light was still on but it ran fine. Light went off while driving to work today I assume one or both sensors need to be replaced, but it doesn't make sense to me that sometimes they would work and sometimes it acts as if there's a complete failure? Worth noting, I replaced the intake book right after I bought it. Not sure about plugs but I'll check next time I'm under the hood.

This is interesting because now that I think about it, the codes seem to come up when it's really humid outside or when it rains. So there might just be a fuse I need to replace?

P.S. - I just re-read the first post and noticed that bit about the battery. I just replaced mine because there were a couple mornings where I had to jump start it, even though the battery was barely a year old. Could a battery really cause an issue like this?