Drain the fluid, drop the pan, pull the filter assembly and clean it good (I just flushed some solvent through it. It's a metal screen so carb cleaner would probably work well enough, but make sure it's good and dry before reinstalling it). Reinstall the filter assembly. Wipe out the inside of the pan and clean off the magnets before putting them back in the pan. Replace the pan with a new cork gasket from Toyota, being sure to use proper torque on the pan bolts. Don't use any RTV or sealers. I never have and have never had a leak. Refill with 5-6 quarts of ATF. I recommend Castrol DexIII/Mercon. Run it and, keeping the ebrake set and while holding the foot brake, shift through each gear. Go from P to 1 and then back up, staying in each gear for 5-7 seconds. Drain the tranny again and refill with synthetic ATF if you can find any. If not then just use Castrol. Be careful to make sure you get the right amount in. You'll probably have to run it a couple times to get fluid up into the lines and through the valve body. It usually takes 6-7 quarts when I do it. This ought to fix any issues with shifting and any irregular behavior in your tranny. I at least change my tranny fluid once a year and have never had any problems with it.
I also HIGHLY recommend you have the factory A440 transmission service manual handy when you drop the pan. And don't bother going in to have your tranny "flushed". It's a waste of good money and it still doesn't get the gunk off the magnets and filter.
Make sure your kickdown cable is working properly if not it could be your throttle vaule body. I was able to just clean mine up and put a new kickdown cable and it's shifted fine ever since (30,000 ago)