2006 Baja NA 4-EAT
Problem: Rough and low idle once warmed up (intermittent). Car would almost stall at times when coming to a stop - not all of the time, but sometimes. Checked all vac hoses, replaced some - problem still existed. Changed spark plugs, air filter, pcv, problem still exited.
Finally I made a correlation that it was slightly harder starting after I filled up with gas (car would start, rpm's would drop, and almost stall (similar to what was experienced when stopping at times).
Armed with that info I replaced the vapor canister purge solenoid (careful buying from Amazon, they don't list the right one for my model). Picked one up from Napa for $90. It's located underneath the intake manifold, but is fairly easy to reach with a socket extension and needle nose pliers for the hoses. Once I replaced this my issues were solved. No more rough idle, no more almost stalling when stopping (intermittent). My car had no CEL which made diagnosing the issue a little more difficult. Hope it helps someone out there.
Fox