2003 5 speed specs in OZ state inspect oil only, and replace oil if "severe service" at 80,000kms or 50,000 miles. I am up to 60000kms and will do the complete fluid change and drop the pan for a look. .... I like to drop the pan, to see what is built up in there, and to remove anything that should not be there.
100 TD - please take some pictures for us so we can decide whether or not this is something the "overmaintain" crowd wants to do.
FSM notes on dropping the pan ...
- be careful not to damage pan flange when removing
- remove the magnets and use them to collect steel particles
- examine the particles in the pan to evaluate wear in the tranmission (Steel - bearing, gear and clutch wear, Brass (non-magnetic) - bushing wear)
- clean the pan with a non-residue cleaner
- Remove all FIPG (formed in place gasket) material from gasket surfaces using a scaper and razor blade
- clean components of all loose material
- clean sealing surfaces with a non-residue solvent (brake cleaner ?)
- do not allow oil on contact surfaces of pan or tranmission case
- when installing apply the FIPG (Toyota part # 08826-00090 or Three Bond 1281) 2-3 mm wide and connect parts within 10 minutes or start over
- even when removed for service the oil strainer is reused but three new gaskets are installed
sounds like there could be benefits to a drain that you don't get with a machine flush.
- gravity drain "backflushes" the strainer
- wear particles at the bottom of the pan are more likely removed
Maybe a drain and fill with a cheap spec fluid would be worthwhile to some even before a "machine exchange".
Watch the fluid exchange in person. Many shops use a machine that removes the old fluid, filters it and then returns it to your transmission. They then add an additive to replenish additives "used up" in the old fluid.
Also look at how the machine is hooked up to the transmission. This decription of how a "top of the line" Snap-on unit operates doesn't sound too good to me. 10 minutes for a $120 service makes good sense to the shop I'm sure!
In a "static" engine off mode, the unit first removes old fluid in the transmission pan through the dipstick, eliminating the messy and timely removal of drain pans. Following fluid removal, the unit then fills the transmission with an equal amount of new fluid through the dipstick. Visible flow meters allow the user to continually monitor fluid movement to and from the transmission. The Snap-on TransKare then prompts the technician to start the engine, during which the unit replaces circulating transmission fluid on a quart-by-quart basis.
The Snap-on TransKare's unique clean and simple dipstick fill and extraction method completes most automatic transmission fluid exchanges within 10 minutes. The automated process adds efficiency and profitability to shops performing transmission fluid services.
It doesn't collect fluid flowing from the cooler output and fill into the pan. It sounds like it removes a quart from the pan, adds a quart by the same tube and repeats until the desired # of quarts have been "exchanged". This is no better than drain and fill a couple of times with a run in between like cary was talking about only without the possible benefit of the drain action. In fact you could do the same with a $9 drill operated lube pump and a section of hose.
I like this method form the 80's FAQ as eventually modified over the course of the thread. Drain and fill to start, Don't run it dry (use an assistant to add fluid as the old pumps out and stop engine as necesary to keep pan filled) and shift through the gears.
80 FAQ thread on ATF exchange using the cooler lines.
I doubt their is any fluid that belongs in both a Toyota T-IV and a Honda ZF-1 tranny. 
