"Changed" brake fluid on an '03, now have to pump pedal sometimes to stop?

You probably need to bleed the ABS pump, that's what the dealer tool probably does.
Go find a sandy lot and do some panic stops, making the ABS go off. See if the brake pedal improves. If it doesn't, follow the factory procedure for bleeding -it's that way for a reason.

 

If you allowed the brake fluid to run dry in the brake fluid reservoir, then air has gotten into the brake actuator and you must follow the prescribed procedure per the Toyota repair manual to bleed the air out.

I changed the brake fluid in my 2001, a few years ago. My procedure was to have my wife very gently depress the brake pedal while I opened up one wheel cylinder valve at a time with a vinyl tube connecting the valve to a glass jar, keeping an eye on the brake fluid reservoir so that it did not drop below 1/2 full. I closed the valve before she released the pedal. This worked amazingly well.

However this procedure would not work on 2G.

 

Then, perhaps you can find a helper and see if the process I suggested above would help to get air out of the system. If the air is only in the lines near the brake wheel cylinders, you might be successful. However as mentioned previously, if you got air into the system via the brake fluid reservoir, forget it.

 

It is not possible to bleed the Gen II brakes without a scan tool or equivalent. There is a complicated procedure, and the tool tells you when to bleed each wheel. It also involves removing the ABS relays. Unless you have the tool, or can borrow one, you will need to go to a dealer or a mechanic that has the tool.

 

Oh, I see you gave a Gen I, My statement above does not apply. This is posted in the Gen II not the Gen I forum. Follow Patrick's instructions.

 

Why do people change their brake fluid?

 

Brake fluid is hydrophilic, so over time water vapor accumulates in the fluid and lowers the boiling point of the fluid. High performance European vehicles usually require a brake fluid change every year or every other year because the maintenance schedule anticipates that your daily driving may be at 100+ mph on the autobahn.