Stumped! INTERMITTEN rough idle

First do a through review of the charging system. Have the battery tested. Have the alternator tested for correct output and excessive AC ripple. Most autoparts stores will do it for free. Don't cut corners on the battery cables. Make sure they are clean and tight.\

Next inspect the spark plug routing. Make SURE that all factory standoffs and looms have been used. Are the wires touching any metal parts?

Clean the MAF. Use only a product designed for the job.

Change the fuel filter.

Change the PCV value.

Check for vacuum leaks. Even a tiny one will cause problems.

Are there any exhaust leaks? If there are any, fix them.

From this point on, things get more complicated and expensive.

Consider an injector cleaning and flow test service such as injectorrx.com. If this is a DD, sending all 6 out at the same time is a problem. Consider buying one new injector and rotate through until all are done.

IMO, it's a common occurance for ppl to replace spark plug wires on the V6 and do a piss poor job of routing. Poorly routed wires still misfire and most ppl stop looking at an ignition problem once the wires have been changed. Do yourself a favor and make sure the ignition system is in tip top shape before moving on.

Don't cut corners on the charging system. You maybe thinking a bad alternator couldn't possiblely have an impact on your problem. Your wrong. It could. The test is free. Rule it out before throwing away money on other things.

Don't make something easy hard. Just rely on the alternator testing equipment. At home, you could test for correct output (generally anything above 13 volts is OK), but it's difficult for the home mechanic to correctly test for AC ripple.