A few corrections:
1st Gens have a 4 spd A/T.
The coolant/ATF mixing problem (SMOD) is more of a 2nd gen problem. I'm not saying it'll never happen with a 1st, but is very, very, VERY unlikely based on the number of vehicles on the road with the problem.
You haven't mentioned if the fluid has been changed or not. A 2003 will likely be approaching 150K, and that long on factory fluid is too long. Fluid changing would be very high on my list at this point. It's a 9 qt system, and approx half will come out with each drain, but be prepared the first time with plenty -- refill with new the same volume that comes out. Drain and fill about a week apart for 4 or 5 times to make certain all the old is out.
Changing the filter is optional as it's more of a screen mesh than a foam or paper filter. Dropping the pan is the only way to clean the magnet, however.
Last edited by muadeeb; 12-11-2012 at 10:11 PM.
Reason: notes about filter