I'd recommend you perform the DIY transmission flush as outlined in several threads including the "shuddering transmission" thread . If you can change your own oil, you can flush the trans in the FJ.And today I tried, one local dealer and was told by mechanic a service bulletin recommends against flush. He offered a drain and fill only.
I am a little conflicted but will continue to search.
I used 3 gallons of fluid (I used Valvoline Maxlife ATF and had great results) and it came out cherry red by the time I was done. The instructions on this forum are spot on.
I also installed a Hayden 679 transmission cooler to keep the new fluid from getting cooked. You can add a cooler at the same time and kill two birds with one stone since you'll have your lines unhooked anyway.