I think you might be a little misinformed here. Toyota did not build any automatic transmissions for the MR2. You have what is called an SMT. This stands for sequential manual transmission. It is a manual with an electro-hydraulic- mechanical clutch. When you pull that gear lever a very complex series of thing take place. It is your clutch but you have no clutch pedal. 00=02 had 5 sp and 03-05n have 6 sp.
All of this being said, it could be your synchros in the transmission. It could be your clutch being worn or it could be one of the control units. Keep your fingers crossed its not one of the control units.
I would get on Spyderchat.com or join the MR2 facebook group. I would hope you have a good mechanic as almost no one can work on the SMT these days so the chats and websites are the best place for answers. You have a very special car with this transmission... I have a 2003 with 6 sp and love it... good luck
I live in St.Pete and probably shouldn't post my email but ajbroome108@gmail.com I am learning my way around the MR2 and doing it quickly and would be happy to help... I am also starting a group for West Coast Syder owners on FB
